boxplotGBSR: Draw boxplots of specified statistics

In tomoyukif/GBScleanR: Error correction tool for noisy genotyping by sequencing (GBS) data

Draw boxplots of specified statistics

Description

Draw boxplots of specified statistics

Usage

boxplotGBSR(
  x,
  stats = "missing",
  target = c("marker", "sample"),
  color = c(Marker = "darkblue", Sample = "darkblue"),
  fill = c(Marker = "skyblue", Sample = "skyblue")
)

Arguments

x	A GbsrGenotypeData object.
stats	A string to specify statistics to be drawn.
target	Either or both of "marker" and "sample", e.g. target = "marker" to draw a histogram only for SNPs.
color	A named vector "Marker" and "Sample" to specify border color of bins in the histograms.
fill	A named vector "Marker" and "Sample" to specify fill color of bins in the histograms.

Details

You can draw boxplots of several summary statistics of genotype counts and read counts per sample and per marker. The "stats" argument can take the following values:

• "missing""Proportion of missing genotype calls.",

• "het""Proportion of heterozygote calls.",

• "raf""Reference allele frequency.",

• "dp""Total read counts.",

• "ad_ref""Reference allele read counts.",

• "ad_alt""Alternative allele read counts.",

• "rrf""Reference allele read frequency.",

• "mean_ref""Mean of reference allele read counts.",

• "sd_ref""Standard deviation of reference allele read counts.",

• "median_ref""Quantile of reference allele read counts.",

• "mean_alt""Mean of alternative allele read counts.",

• "sd_alt""Standard deviation of alternative allele read counts.",

• "median_alt""Quantile of alternative allele read counts.",

• "mq""Mapping quality.",

• "fs""Phred-scaled p-value (strand bias)",

• "qd""Variant Quality by Depth",

• "sor""Symmetric Odds Ratio (strand bias)",

• "mqranksum""Alt vs. Ref read mapping qualities",

• "readposranksum""Alt vs. Ref read position bias",

• "baseqranksum""Alt Vs. Ref base qualities",

To draw boxplots for "missing", "het", "raf", you need to run countGenotype() first to obtain statistics. Similary, "dp", "ad_ref", "ad_alt", "rrf" requires values obtained via countRead(). "mq", "fs", "qd", "sor", "mqranksum", "readposranksum", and "baseqranksum" only work with target = "marker", if your data contains those values supplied via SNP calling tools like GATK.

Value

A ggplot object.

Examples

# Load data in the GDS file and instantiate a [GbsrGenotypeData] object.
gds_fn <- system.file("extdata", "sample.gds", package = "GBScleanR")
gds <- loadGDS(gds_fn)

# Summarize genotype count information to be used in `boxplotGBSR()`
gds <- countGenotype(gds)

boxplotGBSR(gds, stats = "missing")

# Close the connection to the GDS file
closeGDS(gds)

tomoyukif/GBScleanR documentation built on March 12, 2024, 6:27 a.m.