scan1pattern: Plot scan pattern usign ggplot2

In byandell/qtl2pattern: Pattern Support for 'qtl2' Package

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, ...)

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, [e-mail]

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)

byandell/qtl2pattern documentation built on Nov. 9, 2023, 7:57 p.m.