plotCoverage: Plot read coverage and splice junction read counts

In ldg21/SGSeq: Splice event prediction and quantification from RNA-seq data

Description

Plot read coverage and splice junction read counts for an individual sample or averaged across samples.

Usage

plotCoverage(x, geneID = NULL, geneName = NULL, eventID = NULL,
  which = NULL, sample_info = NULL, sizefactor = NA, toscale = c("exon",
  "none", "gene"), color = "darkblue", ylim = NULL, label = NULL,
  nbin = 200, summary = mean, curvature = 1, main = NULL,
  min_anchor = 1, cores = 1)

Arguments

x	SGFeatureCounts or SGFeatures object. If x is an SGFeatureCounts object that includes multiple samples, average coverage and splice junction counts are obtained.
geneID	Single gene identifier used to subset x
geneName	Single gene name used to subset x
eventID	Single event identifier used to subset x
which	GRanges used to subset x
sample_info	Data frame with sample information. If x is an SGFeatureCounts object, sample information is obtained from colData(x). If sample_info includes multiple samples, average coverage and splice junction counts are obtained.
sizefactor	Numeric vector with length equal to the number of samples in sample_info. Used to scale coverages and splice junction counts before plotting, or before averaging across samples. Set to NA to disable scaling. If NULL, size factors are calculated as the number of bases sequenced (the product of library size and average number of bases sequenced per read or fragment), plotted coverages and splice junction counts are per 1 billion sequenced bases.
toscale	Controls which parts of the splice graph are drawn to scale. Possible values are “none” (exonic and intronic regions have constant length), “exon” (exonic regions are drawn to scale) and “gene” (both exonic and intronic regions are drawn to scale).
color	Color used for plotting coverages
ylim	Numeric vector of length two, determining y-axis range used for plotting coverages.
label	Optional y-axis label
nbin	Number of bins for plotting coverages
summary	Function used to calculate per-bin coverage summaries
curvature	Numeric determining curvature of plotted splice junctions.
main	Plot title
min_anchor	Integer specifiying minimum anchor length
cores	Number of cores available for parallel processing.

Value

data.frame with information on splice junctions included in the splice graph

Author(s)

Leonard Goldstein

Examples

## Not run: 
par(mfrow = c(4, 1))
for (j in seq_len(4)) plotCoverage(sgfc_pred[, j])

## End(Not run)
NULL

ldg21/SGSeq documentation built on Oct. 14, 2020, 9:51 p.m.