Package 'qtl2pattern' reference manual

Title:	Pattern Support for 'qtl2' Package
Description:	Routines in 'qtl2' to study allele patterns in quantitative trait loci (QTL) mapping over a chromosome. Useful in crosses with more than two alleles to identify how sets of alleles, genetically different strands at the same locus, have different response levels. Plots show profiles over a chromosome. Can handle multiple traits together. See <https://github.com/byandell/qtl2pattern>.
Authors:	Brian S Yandell [aut, cre]
Maintainer:	Brian S Yandell <[email protected]>
License:	GPL-3
Version:	1.2.2
Built:	2025-02-09 05:16:12 UTC
Source:	https://github.com/byandell-sysgen/qtl2pattern

Allele plot for SNPs, alleles and allele pairs

Description

Create table of alleles for various model fits.

Plot alleles for haplotype, diplotype and top patterns and genome position.

Usage

allele1(
  probD,
  phe_df = NULL,
  cov_mx = NULL,
  map = NULL,
  K_chr = NULL,
  patterns = NULL,
  alt = NULL,
  blups = FALSE,
  ...
)

ggplot_allele1(
  object,
  scan1_object = NULL,
  map = NULL,
  pos = NULL,
  trim = TRUE,
  legend.position = "none",
  ...
)

## S3 method for class 'allele1'
autoplot(object, ...)
allele1(
  probD,
  phe_df = NULL,
  cov_mx = NULL,
  map = NULL,
  K_chr = NULL,
  patterns = NULL,
  alt = NULL,
  blups = FALSE,
  ...
)

ggplot_allele1(
  object,
  scan1_object = NULL,
  map = NULL,
  pos = NULL,
  trim = TRUE,
  legend.position = "none",
  ...
)

## S3 method for class 'allele1'
autoplot(object, ...)

Arguments

`probD`	object of class `calc_genoprob`
`phe_df`	data frame with one phenotype
`cov_mx`	covariate matrix
`map`	Genome map (required if `scan1_object` present).
`K_chr`	kinship matrix
`patterns`	data frame of pattern information
`alt`	Haplotype allele letter(s) for alternative to reference.
`blups`	Create BLUPs if `TRUE`
`...`	Other parameters ignored.
`object`	Object of class `allele1`.
`scan1_object`	Optional object of class `scan1` to find peak.
`pos`	Genome position in Mbp (supercedes `scan1_object`).
`trim`	If `TRUE`, trim extreme alleles.
`legend.position`	Legend position (default is `"none"`).

Value

Table with allele effects across sources.

object of class ggplot

Create a function to query genotype probabilities

Description

Create a function that will connect to a database of genotype probability information and return a list with 'probs' object and a 'map' object.

Usage

create_probs_query_func(dbfile, method_val = "fst", probdir_val = "genoprob")
create_probs_query_func(dbfile, method_val = "fst", probdir_val = "genoprob")

Arguments

`dbfile`	Name of database file
`method_val`	either `"fst"` or `"calc"` for type of genotype probabilities
`probdir_val`	name of probability directory (default `"genoprob"`)

Details

Note that this function assumes that probdir_val has a file with the physical map with positions in Mbp and other files with genotype probabilities. See read_probs for details on how probabilities are read. See create_variant_query_func for original idea.

Value

Function with six arguments, 'chr', 'start', 'end', 'allele', 'method' and 'probdir'. It returns a list with 'probs' and 'map' objects spanning the region specified by the first three arguments. The 'probs' element should be either a 'calc_genoprob' or 'fst_genoprob' object (see fst_genoprob).

Examples

dirpath <- "https://raw.githubusercontent.com/rqtl/qtl2data/master/DOex"

create_qv <- function(dirpath) {
  # Download SNP info for DOex from web via RDS.
  # snpinfo is referenced internally in the created function.
  
  tmpfile <- tempfile()
  download.file(file.path(dirpath, "c2_snpinfo.rds"), tmpfile, quiet=TRUE)
  snpinfo <- readRDS(tmpfile)
  unlink(tmpfile)
  snpinfo <- dplyr::rename(snpinfo, pos = pos_Mbp)
  
  function(chr, start, end) {
    if(chr != "2") return(NULL)
    if(start < 96.5) start <- 96.5
    if(end > 98.5) end <- 98.5
    if(start >= end) return(NULL)
    dplyr::filter(snpinfo, .data$pos >= start, .data$pos <= end)
  }
}

query_variants <- create_qv(dirpath)


create_qg <- function(dirpath) {
  # Download Gene info for DOex from web via RDS
  # gene_tbl is referenced internally in the created function.
  
  tmpfile <- tempfile()
  download.file(file.path(dirpath, "c2_genes.rds"), tmpfile, quiet=TRUE)
  gene_tbl <- readRDS(tmpfile)
  unlink(tmpfile)
  
  function(chr, start, end) {
    if(chr != "2") return(NULL)
    if(start < 96.5) start <- 96.5
    if(end > 98.5) end <- 98.5
    if(start >= end) return(NULL)
    dplyr::filter(gene_tbl, .data$end >= start, .data$start <= end)
  }
}

query_genes <- create_qg(dirpath)


# Examples for probs require either FST or RDS storage of data.

dirpath <- "https://raw.githubusercontent.com/rqtl/qtl2data/master/DOex"

create_qv <- function(dirpath) {
  # Download SNP info for DOex from web via RDS.
  # snpinfo is referenced internally in the created function.
  
  tmpfile <- tempfile()
  download.file(file.path(dirpath, "c2_snpinfo.rds"), tmpfile, quiet=TRUE)
  snpinfo <- readRDS(tmpfile)
  unlink(tmpfile)
  snpinfo <- dplyr::rename(snpinfo, pos = pos_Mbp)
  
  function(chr, start, end) {
    if(chr != "2") return(NULL)
    if(start < 96.5) start <- 96.5
    if(end > 98.5) end <- 98.5
    if(start >= end) return(NULL)
    dplyr::filter(snpinfo, .data$pos >= start, .data$pos <= end)
  }
}

query_variants <- create_qv(dirpath)


create_qg <- function(dirpath) {
  # Download Gene info for DOex from web via RDS
  # gene_tbl is referenced internally in the created function.
  
  tmpfile <- tempfile()
  download.file(file.path(dirpath, "c2_genes.rds"), tmpfile, quiet=TRUE)
  gene_tbl <- readRDS(tmpfile)
  unlink(tmpfile)
  
  function(chr, start, end) {
    if(chr != "2") return(NULL)
    if(start < 96.5) start <- 96.5
    if(end > 98.5) end <- 98.5
    if(start >= end) return(NULL)
    dplyr::filter(gene_tbl, .data$end >= start, .data$start <= end)
  }
}

query_genes <- create_qg(dirpath)


# Examples for probs require either FST or RDS storage of data.

Get exons for set of genes

Description

Match up exon start,stop,strand with genes. Use query_genes to find features; see create_gene_query_func.

Returns table of gene and its exons.

Uses gene_exon to plot genes, exons, mRNA with SNPs.

Usage

gene_exon(
  top_snps_tbl,
  feature_tbl = query_genes(chr_id, range_Mbp[1], range_Mbp[2])
)

## S3 method for class 'gene_exon'
summary(object, gene_name = NULL, top_snps_tbl = NULL, extra = 0.005, ...)

## S3 method for class 'gene_exon'
subset(x, gene_val, ...)

ggplot_gene_exon(
  object,
  top_snps_tbl = NULL,
  plot_now = TRUE,
  genes = unique(object$gene),
  ...
)

## S3 method for class 'gene_exon'
autoplot(object, ...)
gene_exon(
  top_snps_tbl,
  feature_tbl = query_genes(chr_id, range_Mbp[1], range_Mbp[2])
)

## S3 method for class 'gene_exon'
summary(object, gene_name = NULL, top_snps_tbl = NULL, extra = 0.005, ...)

## S3 method for class 'gene_exon'
subset(x, gene_val, ...)

ggplot_gene_exon(
  object,
  top_snps_tbl = NULL,
  plot_now = TRUE,
  genes = unique(object$gene),
  ...
)

## S3 method for class 'gene_exon'
autoplot(object, ...)

Arguments

`top_snps_tbl`	table from `top_snps`
`feature_tbl`	table of features from `query_genes`; see `create_gene_query_func`
`object`	Object of class `gene_exon`.
`gene_name`	name of gene as character string
`extra`	extra region beyond gene for SNPs (in Mbp)
`...`	arguments passed along to `gene_exon`
`x`	Object of class `gene_exon`.
`gene_val`	Name of gene from object `x`.
`plot_now`	plot now if TRUE
`genes`	Names of genes in `object`

Value

tbl of exon and gene features

tbl of summary

list of ggplots (see gene_exon)

Author(s)

Brian S Yandell, [email protected]

Examples

dirpath <- "https://raw.githubusercontent.com/rqtl/qtl2data/master/DOex"

# Read DOex example cross from 'qtl2data'
DOex <- subset(qtl2::read_cross2(file.path(dirpath, "DOex.zip")), chr = "2")


# Download genotype probabilities
tmpfile <- tempfile()
download.file(file.path(dirpath, "DOex_genoprobs_2.rds"), tmpfile, quiet=TRUE)
pr <- readRDS(tmpfile)
unlink(tmpfile)

# Download SNP info for DOex from web and read as RDS.
tmpfile <- tempfile()
download.file(file.path(dirpath, "c2_snpinfo.rds"), tmpfile, quiet=TRUE)
snpinfo <- readRDS(tmpfile)
unlink(tmpfile)
snpinfo <- dplyr::rename(snpinfo, pos = pos_Mbp)

# Convert to SNP probabilities
snpinfo <- qtl2::index_snps(DOex$pmap, snpinfo)
snppr <- qtl2::genoprob_to_snpprob(pr, snpinfo)

# Scan SNPs.
scan_snppr <- qtl2::scan1(snppr, DOex$pheno)

# Collect top SNPs
top_snps_tbl <- top_snps_pattern(scan_snppr, snpinfo)

# Download Gene info for DOex from web via RDS
tmpfile <- tempfile()
download.file(file.path(dirpath, "c2_genes.rds"), tmpfile, quiet=TRUE)
gene_tbl <- readRDS(tmpfile)
unlink(tmpfile)

# Get Gene exon information.
out <- gene_exon(top_snps_tbl, gene_tbl)
summary(out, gene = out$gene[1])


dirpath <- "https://raw.githubusercontent.com/rqtl/qtl2data/master/DOex"

# Read DOex example cross from 'qtl2data'
DOex <- subset(qtl2::read_cross2(file.path(dirpath, "DOex.zip")), chr = "2")


# Download genotype probabilities
tmpfile <- tempfile()
download.file(file.path(dirpath, "DOex_genoprobs_2.rds"), tmpfile, quiet=TRUE)
pr <- readRDS(tmpfile)
unlink(tmpfile)

# Download SNP info for DOex from web and read as RDS.
tmpfile <- tempfile()
download.file(file.path(dirpath, "c2_snpinfo.rds"), tmpfile, quiet=TRUE)
snpinfo <- readRDS(tmpfile)
unlink(tmpfile)
snpinfo <- dplyr::rename(snpinfo, pos = pos_Mbp)

# Convert to SNP probabilities
snpinfo <- qtl2::index_snps(DOex$pmap, snpinfo)
snppr <- qtl2::genoprob_to_snpprob(pr, snpinfo)

# Scan SNPs.
scan_snppr <- qtl2::scan1(snppr, DOex$pheno)

# Collect top SNPs
top_snps_tbl <- top_snps_pattern(scan_snppr, snpinfo)

# Download Gene info for DOex from web via RDS
tmpfile <- tempfile()
download.file(file.path(dirpath, "c2_genes.rds"), tmpfile, quiet=TRUE)
gene_tbl <- readRDS(tmpfile)
unlink(tmpfile)

# Get Gene exon information.
out <- gene_exon(top_snps_tbl, gene_tbl)
summary(out, gene = out$gene[1])

Collapse genoprob according to pattern

Description

Collapse genoprob according to pattern

Usage

genoprob_to_patternprob(probs1, sdp, alleles = FALSE)
genoprob_to_patternprob(probs1, sdp, alleles = FALSE)

Arguments

`probs1`	object of class `calc_genoprob`
`sdp`	SNP distribution pattern
`alleles`	use allele string if `TRUE`

Value

object of class calc_genoprob

Author(s)

Brian S Yandell, [email protected]

Examples

dirpath <- "https://raw.githubusercontent.com/rqtl/qtl2data/master/DOex"

# Read DOex example cross from 'qtl2data'
DOex <- subset(qtl2::read_cross2(file.path(dirpath, "DOex.zip")), chr = "2")


# Download genotype probabilities
tmpfile <- tempfile()
download.file(file.path(dirpath, "DOex_genoprobs_2.rds"), tmpfile, quiet=TRUE)
pr <- readRDS(tmpfile)
unlink(tmpfile)

# Convert genotype probabilities to pattern probabilities for pattern 1.
pattern_pr <- genoprob_to_patternprob(pr, 7, TRUE)

str(pr)
str(pattern_pr)


dirpath <- "https://raw.githubusercontent.com/rqtl/qtl2data/master/DOex"

# Read DOex example cross from 'qtl2data'
DOex <- subset(qtl2::read_cross2(file.path(dirpath, "DOex.zip")), chr = "2")


# Download genotype probabilities
tmpfile <- tempfile()
download.file(file.path(dirpath, "DOex_genoprobs_2.rds"), tmpfile, quiet=TRUE)
pr <- readRDS(tmpfile)
unlink(tmpfile)

# Convert genotype probabilities to pattern probabilities for pattern 1.
pattern_pr <- genoprob_to_patternprob(pr, 7, TRUE)

str(pr)
str(pattern_pr)

Match features with SNPs

Description

Find features that overlap with SNPs

Usage

get_feature_snp(snp_tbl, feature_tbl, extend = 0.005)
get_feature_snp(snp_tbl, feature_tbl, extend = 0.005)

Arguments

`snp_tbl`	tbl of SNPs from `assoc.map`
`feature_tbl`	tbl of feature information from `create_gene_query_func`
`extend`	extend region for SNPs in Mbp (default 0.005)

Value

tbl of features covering SNPs

Author(s)

Brian S Yandell, [email protected]

Match genes with SNPs

Description

Internal routine to find features that overlap with SNPs

Usage

get_gene_snp(
  snp_tbl,
  feature_tbl,
  feature_snp = get_feature_snp(snp_tbl, feature_tbl, 0)
)
get_gene_snp(
  snp_tbl,
  feature_tbl,
  feature_snp = get_feature_snp(snp_tbl, feature_tbl, 0)
)

Arguments

`snp_tbl`	tbl of SNPs from `query_variants`; see package `create_variant_query_func`
`feature_tbl`	tbl of feature information from `query_genes`; see package `create_gene_query_func`
`feature_snp`	tbl of feature information from `get_feature_snp`

Value

tbl of genes covering SNPs

Author(s)

Brian S Yandell, [email protected]

Helper function to set gene locations on plot.

Description

Figure out gene locations to make room for gene names. Written original by Dan Gatti 2013-02-13

Usage

get.gene.locations(
  locs,
  xlim,
  text_size = 3,
  str_rect = c("iW", "i"),
  n_rows = 10,
  plot_width = 6,
  ...
)
get.gene.locations(
  locs,
  xlim,
  text_size = 3,
  str_rect = c("iW", "i"),
  n_rows = 10,
  plot_width = 6,
  ...
)

Arguments

`locs`	tbl of gene information
`xlim`	X axis limits
`text_size`	size of text (default 3)
`str_rect`	character spacing on left and right of rectangles (default c("iW","i"))
`n_rows`	desired number of rows (default 10)
`plot_width`	width of default plot window (in inches)
`...`	additional parameters (not used)

Value

list object used by ggplot_feature_tbl

Author(s)

Brian S Yandell, [email protected] Daniel Gatti, [email protected]

References

https://github.com/dmgatti/DOQTL/blob/master/R/gene.plot.R

Plot of merge_feature object

Description

Merge all SNPs in small region with LOD peaks across multiple phenotype.

Usage

ggplot_merge_feature(object, pheno, plot_by = c("pattern", "consequence"), ...)

## S3 method for class 'merge_feature'
autoplot(object, ...)

merge_feature(
  top_snps_tbl,
  snpinfo,
  out_lmm_snps,
  drop = 1.5,
  dropchar = 0,
  exons = gene_exon(top_snps_tbl)
)

## S3 method for class 'merge_feature'
summary(object, sum_type = c("SNP type", "pattern"), ...)
ggplot_merge_feature(object, pheno, plot_by = c("pattern", "consequence"), ...)

## S3 method for class 'merge_feature'
autoplot(object, ...)

merge_feature(
  top_snps_tbl,
  snpinfo,
  out_lmm_snps,
  drop = 1.5,
  dropchar = 0,
  exons = gene_exon(top_snps_tbl)
)

## S3 method for class 'merge_feature'
summary(object, sum_type = c("SNP type", "pattern"), ...)

Arguments

`object`	of class `merge_feature`
`pheno`	name of phenotype to be plotted
`plot_by`	element to plot by (one of `c("pattern","consequence")`)
`...`	other arguments not used
`top_snps_tbl`	tbl from `top_snps_pattern` or `top_snps`
`snpinfo`	SNP information table
`out_lmm_snps`	tbl from `scan1` on SNPs
`drop`	include LOD scores within `drop` of max for each phenotype
`dropchar`	number of characters to drop on phenames
`exons`	table from `gene_exon`
`sum_type`	one of `c("SNP type","pattern")`

Value

ggplot2 object

tbl with added information on genes and exons

table summary

Author(s)

Brian S Yandell, [email protected]

Examples

dirpath <- "https://raw.githubusercontent.com/rqtl/qtl2data/master/DOex"

# Read DOex example cross from 'qtl2data'
DOex <- subset(qtl2::read_cross2(file.path(dirpath, "DOex.zip")), chr = "2")


# Download genotype probabilities
tmpfile <- tempfile()
download.file(file.path(dirpath, "DOex_genoprobs_2.rds"), tmpfile, quiet=TRUE)
pr <- readRDS(tmpfile)
unlink(tmpfile)

# Download SNP info for DOex from web and read as RDS.
tmpfile <- tempfile()
download.file(file.path(dirpath, "c2_snpinfo.rds"), tmpfile, quiet=TRUE)
snpinfo <- readRDS(tmpfile)
unlink(tmpfile)
snpinfo <- dplyr::rename(snpinfo, pos = pos_Mbp)

# Convert to SNP probabilities
snpinfo <- qtl2::index_snps(DOex$pmap, snpinfo)
snppr <- qtl2::genoprob_to_snpprob(pr, snpinfo)

# Scan SNPs.
scan_snppr <- qtl2::scan1(snppr, DOex$pheno)

# Collect top SNPs
top_snps_tbl <- top_snps_pattern(scan_snppr, snpinfo)
summary(top_snps_tbl)

# Download Gene info for DOex from web via RDS
tmpfile <- tempfile()
download.file(file.path(dirpath, "c2_genes.rds"), tmpfile, quiet=TRUE)
gene_tbl <- readRDS(tmpfile)
unlink(tmpfile)

out <- merge_feature(top_snps_tbl, snpinfo, scan_snppr, exons = gene_tbl)
summary(out, "pattern")


dirpath <- "https://raw.githubusercontent.com/rqtl/qtl2data/master/DOex"

# Read DOex example cross from 'qtl2data'
DOex <- subset(qtl2::read_cross2(file.path(dirpath, "DOex.zip")), chr = "2")


# Download genotype probabilities
tmpfile <- tempfile()
download.file(file.path(dirpath, "DOex_genoprobs_2.rds"), tmpfile, quiet=TRUE)
pr <- readRDS(tmpfile)
unlink(tmpfile)

# Download SNP info for DOex from web and read as RDS.
tmpfile <- tempfile()
download.file(file.path(dirpath, "c2_snpinfo.rds"), tmpfile, quiet=TRUE)
snpinfo <- readRDS(tmpfile)
unlink(tmpfile)
snpinfo <- dplyr::rename(snpinfo, pos = pos_Mbp)

# Convert to SNP probabilities
snpinfo <- qtl2::index_snps(DOex$pmap, snpinfo)
snppr <- qtl2::genoprob_to_snpprob(pr, snpinfo)

# Scan SNPs.
scan_snppr <- qtl2::scan1(snppr, DOex$pheno)

# Collect top SNPs
top_snps_tbl <- top_snps_pattern(scan_snppr, snpinfo)
summary(top_snps_tbl)

# Download Gene info for DOex from web via RDS
tmpfile <- tempfile()
download.file(file.path(dirpath, "c2_genes.rds"), tmpfile, quiet=TRUE)
gene_tbl <- readRDS(tmpfile)
unlink(tmpfile)

out <- merge_feature(top_snps_tbl, snpinfo, scan_snppr, exons = gene_tbl)
summary(out, "pattern")

Plot scan pattern usign ggplot2

Description

Plot scan pattern usign ggplot2

Genome scan by pattern set

Usage

ggplot_scan1pattern(
  object,
  map,
  plot_type = c("lod", "coef", "coef_and_lod"),
  patterns = object$patterns$founders,
  columns = 1:3,
  min_lod = 3,
  lodcolumn = seq_along(patterns),
  facet = "pheno",
  ...
)

## S3 method for class 'scan1pattern'
autoplot(object, ...)

scan1pattern(
  probs1,
  phe,
  K = NULL,
  covar = NULL,
  map,
  patterns,
  condense_patterns = TRUE,
  blups = FALSE,
  do_scans = TRUE
)

## S3 method for class 'scan1pattern'
summary(object, map, ...)
ggplot_scan1pattern(
  object,
  map,
  plot_type = c("lod", "coef", "coef_and_lod"),
  patterns = object$patterns$founders,
  columns = 1:3,
  min_lod = 3,
  lodcolumn = seq_along(patterns),
  facet = "pheno",
  ...
)

## S3 method for class 'scan1pattern'
autoplot(object, ...)

scan1pattern(
  probs1,
  phe,
  K = NULL,
  covar = NULL,
  map,
  patterns,
  condense_patterns = TRUE,
  blups = FALSE,
  do_scans = TRUE
)

## S3 method for class 'scan1pattern'
summary(object, map, ...)

Arguments

`object`	object of class `scan1pattern`
`map`	genome map
`plot_type`	type of plot from `c("lod","coef")`
`patterns`	data frame of pattern information
`columns`	columns used for coef plot
`min_lod`	minimum LOD peak for contrast to be retained
`lodcolumn`	columns used for scan1 plot (default all `patterns`)
`facet`	Plot facets if multiple phenotypes and patterns provided (default = `"pheno"`).
`...`	additional parameters passed on to other methods
`probs1`	object of class `calc_genoprob`
`phe`	data frame with one phenotype
`K`	kinship matrix
`covar`	covariate matrix
`condense_patterns`	remove snp_action from contrasts if TRUE
`blups`	Create BLUPs if `TRUE`
`do_scans`	Do scans if `TRUE`.

Value

object of class ggplot

List containing:

patterns Data frame of summary for top patterns (column founders has pattern)
dip_set Diplotype sets for contrasts
group Group for each founder pattern
scan Object of class scan1.
coef Object of class listof_scan1coef. See package 'qtl2ggplot'.

Author(s)

Brian S Yandell, [email protected]

Examples

dirpath <- "https://raw.githubusercontent.com/rqtl/qtl2data/master/DOex"

# Read DOex example cross from 'qtl2data'
DOex <- subset(qtl2::read_cross2(file.path(dirpath, "DOex.zip")), chr = "2")


# Download genotype probabilities
tmpfile <- tempfile()
download.file(file.path(dirpath, "DOex_genoprobs_2.rds"), tmpfile, quiet=TRUE)
pr <- readRDS(tmpfile)
unlink(tmpfile)

# Download SNP info for DOex from web and read as RDS.
tmpfile <- tempfile()
download.file(file.path(dirpath, "c2_snpinfo.rds"), tmpfile, quiet=TRUE)
snpinfo <- readRDS(tmpfile)
unlink(tmpfile)
snpinfo <- dplyr::rename(snpinfo, pos = pos_Mbp)

# Convert to SNP probabilities
snpinfo <- qtl2::index_snps(DOex$pmap, snpinfo)
snppr <- qtl2::genoprob_to_snpprob(pr, snpinfo)

# Scan SNPs
scan_snppr <- qtl2::scan1(snppr, DOex$pheno)
top_snps_tbl <- top_snps_pattern(scan_snppr, snpinfo)

# Summarize to find top patterns
patterns <- dplyr::arrange(summary(top_snps_tbl), dplyr::desc(max_lod))

# Scan using patterns.
scan_pat <- scan1pattern(pr, DOex$pheno, map = DOex$pmap, patterns = patterns)

# Summary of scan1pattern.
summary(scan_pat, DOex$pmap)


dirpath <- "https://raw.githubusercontent.com/rqtl/qtl2data/master/DOex"

# Read DOex example cross from 'qtl2data'
DOex <- subset(qtl2::read_cross2(file.path(dirpath, "DOex.zip")), chr = "2")


# Download genotype probabilities
tmpfile <- tempfile()
download.file(file.path(dirpath, "DOex_genoprobs_2.rds"), tmpfile, quiet=TRUE)
pr <- readRDS(tmpfile)
unlink(tmpfile)

# Download SNP info for DOex from web and read as RDS.
tmpfile <- tempfile()
download.file(file.path(dirpath, "c2_snpinfo.rds"), tmpfile, quiet=TRUE)
snpinfo <- readRDS(tmpfile)
unlink(tmpfile)
snpinfo <- dplyr::rename(snpinfo, pos = pos_Mbp)

# Convert to SNP probabilities
snpinfo <- qtl2::index_snps(DOex$pmap, snpinfo)
snppr <- qtl2::genoprob_to_snpprob(pr, snpinfo)

# Scan SNPs
scan_snppr <- qtl2::scan1(snppr, DOex$pheno)
top_snps_tbl <- top_snps_pattern(scan_snppr, snpinfo)

# Summarize to find top patterns
patterns <- dplyr::arrange(summary(top_snps_tbl), dplyr::desc(max_lod))

# Scan using patterns.
scan_pat <- scan1pattern(pr, DOex$pheno, map = DOex$pmap, patterns = patterns)

# Summary of scan1pattern.
summary(scan_pat, DOex$pmap)

Extract pattern of diplotypes

Description

Extract pattern of diplotypes

Extract pattern of haplotypes

Usage

pattern_diplos(sdp, haplos, diplos, cont = NULL)

pattern_haplos(sdp, haplos)
pattern_diplos(sdp, haplos, diplos, cont = NULL)

pattern_haplos(sdp, haplos)

Arguments

`sdp`	vector of sdp from `top_snps_pattern`
`haplos`	vector of haplotype names
`diplos`	vector of diplotype names
`cont`	vector of types of contrasts (`NULL` or from `c("add","dom","b6r","b6d")`)

Value

matrix of diplotype patterns

matrix of haplotype patterns

Author(s)

Brian S Yandell, [email protected]

Turn genotype probabilities into labels

Description

Turn genotype probabilities into labels

Usage

pattern_label(genos, allele = TRUE)

pattern_sdp(label, sdp = NULL, geno_names = sort(unique(label)))
pattern_label(genos, allele = TRUE)

pattern_sdp(label, sdp = NULL, geno_names = sort(unique(label)))

Arguments

`genos`	matrix of genotype probabilities at locus
`allele`	Driver has alleles if `TRUE`, otherwise allele pairs.
`label`	character string from `pattern_label`
`sdp`	SNP distribution pattern for plot colors
`geno_names`	unique genotype names (alleles or allele pairs)

Value

character vector of genotype names.

Read fast database with possible rownames

Description

Read fast database with format fst. Use first column of database (must be named 'ind') as rownames if desired. R/qtl2 routines assume data frames have rownames to use to align individuals.

Usage

read_fast(datapath, columns = NULL, rownames = TRUE)
read_fast(datapath, columns = NULL, rownames = TRUE)

Arguments

`datapath`	character string path to database
`columns`	names or indexes for columns to be extracted
`rownames`	use first column of rownames if `TRUE` (can supply column number)

Value

extracted data frame with appropriate rows and columns.

Read genotype probability object from file

Description

Read object from file stored according to method.

Usage

read_probs(
  chr = NULL,
  start_val = NULL,
  end_val = NULL,
  datapath,
  allele = TRUE,
  method,
  probdir = "genoprob"
)
read_probs(
  chr = NULL,
  start_val = NULL,
  end_val = NULL,
  datapath,
  allele = TRUE,
  method,
  probdir = "genoprob"
)

Arguments

`chr`	vector of chromosome identifiers
`start_val`, `end_val`	start and end values in Mbp
`datapath`	name of folder with Derived Data
`allele`	read haplotype allele probabilities (if `TRUE`) or diplotype allele-pair probabilities (if `FALSE`)
`method`	method of genoprob storage
`probdir`	genotype probability directory (default `"genoprob"`)

Value

list with probs = large object of class calc_genoprob and map = physical map for selected chr

Author(s)

Brian S Yandell, [email protected]

Convert sdp to pattern

Description

Convert strain distribution pattern (sdp) to letter pattern.

Usage

sdp_to_pattern(sdp, haplos, symmetric = TRUE)

sdp_to_logical(sdp, haplos, symmetric = TRUE)
sdp_to_pattern(sdp, haplos, symmetric = TRUE)

sdp_to_logical(sdp, haplos, symmetric = TRUE)

Arguments

`sdp`	vector of sdp values
`haplos`	letter codes for haplotypes (required)
`symmetric`	make patterns symmetric if `TRUE`

Value

vector of letter patterns

Author(s)

Brian S Yandell, [email protected]

Examples

dirpath <- "https://raw.githubusercontent.com/rqtl/qtl2data/master/DOex"


# Download SNP info for DOex from web and read as RDS.
tmpfile <- tempfile()
download.file(file.path(dirpath, "c2_snpinfo.rds"), tmpfile, quiet=TRUE)
snpinfo <- readRDS(tmpfile)
unlink(tmpfile)
snpinfo <- dplyr::rename(snpinfo, pos = pos_Mbp)

# Extract strain distribution pattern.
sdp <- snpinfo$sdp
# Find out how many alleles.
nallele <- ceiling(log2(max(sdp)))
out <- sdp_to_pattern(sdp, LETTERS[seq_len(nallele)])
# Show most frequent patterns. 
head(rev(sort(c(table(out)))))


dirpath <- "https://raw.githubusercontent.com/rqtl/qtl2data/master/DOex"


# Download SNP info for DOex from web and read as RDS.
tmpfile <- tempfile()
download.file(file.path(dirpath, "c2_snpinfo.rds"), tmpfile, quiet=TRUE)
snpinfo <- readRDS(tmpfile)
unlink(tmpfile)
snpinfo <- dplyr::rename(snpinfo, pos = pos_Mbp)

# Extract strain distribution pattern.
sdp <- snpinfo$sdp
# Find out how many alleles.
nallele <- ceiling(log2(max(sdp)))
out <- sdp_to_pattern(sdp, LETTERS[seq_len(nallele)])
# Show most frequent patterns. 
head(rev(sort(c(table(out)))))

Convert SNP info to map

Description

Convert SNP info to map

Usage

snpinfo_to_map(snpinfo)
snpinfo_to_map(snpinfo)

Arguments

snpinfo

Data frame with SNP information with the following columns (the last three are generally derived from with index_snps):

chr - Character string or factor with chromosome
pos - Position (in same units as in the "map" attribute in genoprobs.
sdp - Strain distribution pattern: an integer, between 1 and $2^n - 2$ where $n$ is the number of strains, whose binary encoding indicates the founder genotypes
snp - Character string with SNP identifier (if missing, the rownames are used).
index - Indices that indicate equivalent groups of SNPs.
intervals - Indexes that indicate which marker intervals the SNPs reside.
on_map - Indicate whether SNP coincides with a marker in the genoprobs

Value

map as list of vectors of marker positions.

Collapse genoprob according to pattern

Description

Collapse genoprob according to pattern

Usage

snpprob_collapse(
  snpprobs,
  action = c("additive", "add+dom", "non-add", "recessive", "dominant", "basic")
)
snpprob_collapse(
  snpprobs,
  action = c("additive", "add+dom", "non-add", "recessive", "dominant", "basic")
)

Arguments

`snpprobs`	object of class `calc_genoprob`
`action`	SNP gene action type

Value

object of class calc_genoprob

Author(s)

Brian S Yandell, [email protected]

Examples

dirpath <- "https://raw.githubusercontent.com/rqtl/qtl2data/master/DOex"

# Read DOex example cross from 'qtl2data'
DOex <- subset(qtl2::read_cross2(file.path(dirpath, "DOex.zip")), chr = "2")


# Download genotype probabilities
tmpfile <- tempfile()
download.file(file.path(dirpath, "DOex_genoprobs_2.rds"), tmpfile, quiet=TRUE)
pr <- readRDS(tmpfile)
unlink(tmpfile)

# Download SNP info for DOex from web and read as RDS.
tmpfile <- tempfile()
download.file(file.path(dirpath, "c2_snpinfo.rds"), tmpfile, quiet=TRUE)
snpinfo <- readRDS(tmpfile)
unlink(tmpfile)
snpinfo <- dplyr::rename(snpinfo, pos = pos_Mbp)

# Convert to snp probabilities
snpinfo <- qtl2::index_snps(DOex$pmap, snpinfo)
snppr <- qtl2::genoprob_to_snpprob(pr, snpinfo)


dim(snppr[[1]])
dim(snpprob_collapse(snppr, "additive")[[1]])


dirpath <- "https://raw.githubusercontent.com/rqtl/qtl2data/master/DOex"

# Read DOex example cross from 'qtl2data'
DOex <- subset(qtl2::read_cross2(file.path(dirpath, "DOex.zip")), chr = "2")


# Download genotype probabilities
tmpfile <- tempfile()
download.file(file.path(dirpath, "DOex_genoprobs_2.rds"), tmpfile, quiet=TRUE)
pr <- readRDS(tmpfile)
unlink(tmpfile)

# Download SNP info for DOex from web and read as RDS.
tmpfile <- tempfile()
download.file(file.path(dirpath, "c2_snpinfo.rds"), tmpfile, quiet=TRUE)
snpinfo <- readRDS(tmpfile)
unlink(tmpfile)
snpinfo <- dplyr::rename(snpinfo, pos = pos_Mbp)

# Convert to snp probabilities
snpinfo <- qtl2::index_snps(DOex$pmap, snpinfo)
snppr <- qtl2::genoprob_to_snpprob(pr, snpinfo)


dim(snppr[[1]])
dim(snpprob_collapse(snppr, "additive")[[1]])

Summary of features with SNP information

Description

Summary of features with SNP information

Usage

## S3 method for class 'feature_snp'
summary(object, ...)
## S3 method for class 'feature_snp'
summary(object, ...)

Arguments

`object`	tbl of feature information from `get_feature_snp`
`...`	additional parameters ignored

Value

tbl of feature summaries by type

Author(s)

Brian S Yandell, [email protected]

Summary of features

Description

Show count min and max of features by type

Plot genes as rectangles followed by names. Stagger genes for easy reading. Written original by Dan Gatti 2013-02-13

Usage

## S3 method for class 'feature_tbl'
summary(object, major = TRUE, ...)

## S3 method for class 'feature_tbl'
subset(x, start_val = 0, stop_val = max(x$stop), ...)

ggplot_feature_tbl(
  object,
  rect_col = "grey70",
  strand_col = c(`-` = "#1b9e77", `+` = "#d95f02"),
  type_col = c(gene = "black", pseudogene = "#1b9e77", other = "#d95f02"),
  text_size = 3,
  xlim = NULL,
  snp_pos = top_snps_tbl$pos,
  snp_lod = top_snps_tbl$lod,
  top_snps_tbl = NULL,
  snp_col = "grey70",
  extend = 0.005,
  ...
)

## S3 method for class 'feature_tbl'
autoplot(object, ...)
## S3 method for class 'feature_tbl'
summary(object, major = TRUE, ...)

## S3 method for class 'feature_tbl'
subset(x, start_val = 0, stop_val = max(x$stop), ...)

ggplot_feature_tbl(
  object,
  rect_col = "grey70",
  strand_col = c(`-` = "#1b9e77", `+` = "#d95f02"),
  type_col = c(gene = "black", pseudogene = "#1b9e77", other = "#d95f02"),
  text_size = 3,
  xlim = NULL,
  snp_pos = top_snps_tbl$pos,
  snp_lod = top_snps_tbl$lod,
  top_snps_tbl = NULL,
  snp_col = "grey70",
  extend = 0.005,
  ...
)

## S3 method for class 'feature_tbl'
autoplot(object, ...)

Arguments

`object`	tbl of gene information from `query_variants`; see `create_variant_query_func`
`major`	if `TRUE` (default), only summarize genes and exons
`...`	additional arguments (not used)
`x`	tbl of feature information from `get_feature_snp`
`start_val`, `stop_val`	start and stop positions for subset
`rect_col`	fill color of rectangle (default "grey70")
`strand_col`	edge color of rectangle by strand from `object` (default -="blue", +="red"; none if NULL)
`type_col`	color of type from `object` (default "black" for gene, "blue" for pseudogene; none if NULL)
`text_size`	size of text (default 3)
`xlim`	horizontal axis limits (default is range of features)
`snp_pos`	position of SNPs in bp if used (default NULL)
`snp_lod`	LOD of SNPs (for color plotting)
`top_snps_tbl`	table from `top_snps`
`snp_col`	color of SNP vertical lines (default "grey70")
`extend`	extend region for SNPs in bp (default 0.005)

Value

tbl of feature summaries by type

data frame of gene information (invisible)

Author(s)

Brian S Yandell, [email protected]

Brian S Yandell, [email protected] Daniel Gatti, [email protected]

References

https://github.com/dmgatti/DOQTL/blob/master/R/gene.plot.R

Summary of genes overlapping SNPs

Description

Summary of genes overlapping SNPs

Usage

## S3 method for class 'gene_snp'
summary(object, ...)
## S3 method for class 'gene_snp'
summary(object, ...)

Arguments

`object`	tbl of feature information from `get_feature_snp`
`...`	additional parameters ignored

Value

tbl of feature summaries by type

Author(s)

Brian S Yandell, [email protected]

Top SNPs organized by allele pattern

Description

Separate fine mapping scans by allele pattern.

Usage

top_snps_pattern(
  scan1_output,
  snpinfo,
  drop = 1.5,
  show_all_snps = TRUE,
  haplos
)

## S3 method for class 'top_snps_pattern'
summary(object, sum_type = c("range", "best", "peak"), ...)

## S3 method for class 'top_snps_pattern'
subset(x, start_val = 0, end_val = max(x$pos), pheno = NULL, ...)
top_snps_pattern(
  scan1_output,
  snpinfo,
  drop = 1.5,
  show_all_snps = TRUE,
  haplos
)

## S3 method for class 'top_snps_pattern'
summary(object, sum_type = c("range", "best", "peak"), ...)

## S3 method for class 'top_snps_pattern'
subset(x, start_val = 0, end_val = max(x$pos), pheno = NULL, ...)

Arguments

`scan1_output`	output of linear mixed model for `phename` (see `scan1`)
`snpinfo`	Data frame with SNP information with the following columns (the last three are generally derived from with `index_snps`): `chr` - Character string or factor with chromosome `pos` - Position (in same units as in the `"map"` attribute in `genoprobs`. `sdp` - Strain distribution pattern: an integer, between 1 and $2^n - 2$ where $n$ is the number of strains, whose binary encoding indicates the founder genotypes `snp_id` - Character string with SNP identifier (if missing, the rownames are used). `index` - Indices that indicate equivalent groups of SNPs. `intervals` - Indexes that indicate which marker intervals the SNPs reside. `on_map` - Indicate whether SNP coincides with a marker in the `genoprobs`
`drop`	include all SNPs within `drop` of max LOD (default 1.5)
`show_all_snps`	show all SNPs if `TRUE`
`haplos`	optional argument identify codes for haplotypes
`object`	object of class `top_snps_tbl`
`sum_type`	type of summary (one of "range","best")
`...`	additional parameters ignored
`x`	tbl of feature information from `get_feature_snp`
`start_val`, `end_val`	start and end positions for subset
`pheno`	phenotype name(s) for subset

Value

table of top_snps at maximum lod for pattern

table summary

subset of x

Author(s)

Brian S Yandell, [email protected]

Examples

dirpath <- "https://raw.githubusercontent.com/rqtl/qtl2data/master/DOex"

# Read DOex example cross from 'qtl2data'
DOex <- subset(qtl2::read_cross2(file.path(dirpath, "DOex.zip")), chr = "2")


# Download genotype probabilities
tmpfile <- tempfile()
download.file(file.path(dirpath, "DOex_genoprobs_2.rds"), tmpfile, quiet=TRUE)
pr <- readRDS(tmpfile)
unlink(tmpfile)

# Download SNP info for DOex from web and read as RDS.
tmpfile <- tempfile()
download.file(file.path(dirpath, "c2_snpinfo.rds"), tmpfile, quiet=TRUE)
snpinfo <- readRDS(tmpfile)
unlink(tmpfile)
snpinfo <- dplyr::rename(snpinfo, pos = pos_Mbp)

# Convert to SNP probabilities
snpinfo <- qtl2::index_snps(DOex$pmap, snpinfo)
snppr <- qtl2::genoprob_to_snpprob(pr, snpinfo)

# Scan SNPs.
scan_snppr <- qtl2::scan1(snppr, DOex$pheno)

# Collect top SNPs
top_snps_tbl <- top_snps_pattern(scan_snppr, snpinfo)
summary(top_snps_tbl)


dirpath <- "https://raw.githubusercontent.com/rqtl/qtl2data/master/DOex"

# Read DOex example cross from 'qtl2data'
DOex <- subset(qtl2::read_cross2(file.path(dirpath, "DOex.zip")), chr = "2")


# Download genotype probabilities
tmpfile <- tempfile()
download.file(file.path(dirpath, "DOex_genoprobs_2.rds"), tmpfile, quiet=TRUE)
pr <- readRDS(tmpfile)
unlink(tmpfile)

# Download SNP info for DOex from web and read as RDS.
tmpfile <- tempfile()
download.file(file.path(dirpath, "c2_snpinfo.rds"), tmpfile, quiet=TRUE)
snpinfo <- readRDS(tmpfile)
unlink(tmpfile)
snpinfo <- dplyr::rename(snpinfo, pos = pos_Mbp)

# Convert to SNP probabilities
snpinfo <- qtl2::index_snps(DOex$pmap, snpinfo)
snppr <- qtl2::genoprob_to_snpprob(pr, snpinfo)

# Scan SNPs.
scan_snppr <- qtl2::scan1(snppr, DOex$pheno)

# Collect top SNPs
top_snps_tbl <- top_snps_pattern(scan_snppr, snpinfo)
summary(top_snps_tbl)

Package 'qtl2pattern'

Help Index

Allele plot for SNPs, alleles and allele pairs

Description

Usage

Arguments

Value

Create a function to query genotype probabilities

Description

Usage

Arguments

Details

Value

Examples

Get exons for set of genes

Description

Usage

Arguments

Value

Author(s)

Examples

Collapse genoprob according to pattern

Description

Usage

Arguments

Value

Author(s)

Examples

Match features with SNPs

Description

Usage

Arguments

Value

Author(s)

Match genes with SNPs

Description

Usage

Arguments

Value

Author(s)

Helper function to set gene locations on plot.

Description

Usage

Arguments

Value

Author(s)

References

Plot of merge_feature object

Description

Usage

Arguments

Value

Author(s)

Examples

Plot scan pattern usign ggplot2

Description

Usage

Arguments

Value

Author(s)

Examples

Extract pattern of diplotypes

Description

Usage

Arguments

Value

Author(s)

Turn genotype probabilities into labels

Description

Usage

Arguments

Value

Read fast database with possible rownames

Description

Usage

Arguments

Value

See Also

Read genotype probability object from file

Description