pSitePlot {ORFik}R Documentation

Plot area around TIS for p-shifted reads

Description

Usefull to validate p-shifting is correct Can be used for any coverage of region around a point, like TIS, TSS, stop site etc.

Usage

pSitePlot(hitMap, length = 29, region = "start", output = NULL)

Arguments

hitMap

a data.frame/data.table, given from metaWindow (must have columns: position, (score or count) and frame)

length

an integer (29), which length is this for?

region

a character (start), either "start or "stop"

output

character string (NULL), if set, saves the plot as pdf or png to path given. If no format is given, is save as pdf.

Value

a ggplot object of the coverage plot, NULL if output is set, then the plot will only be saved to location.

See Also

Other coveragePlot: coverageHeatMap, savePlot, windowCoveragePlot

Examples

# An ORF
grl <- GRangesList(tx1 = GRanges("1", IRanges(1, 6), "+"))
# Ribo-seq reads
range <- IRanges(c(rep(1, 3), 2, 3, rep(4, 2), 5, 6), width = 1 )
reads <- GRanges("1", range, "+")
coverage <- coveragePerTiling(grl, reads, TRUE, as.data.table = TRUE,
                              withFrames = TRUE)
ORFik:::pSitePlot(coverage)

# See vignette for more examples


[Package ORFik version 1.4.0 Index]