pSitePlot {ORFik} | R Documentation |
Usefull to validate p-shifting is correct Can be used for any coverage of region around a point, like TIS, TSS, stop site etc.
pSitePlot(hitMap, length = 29, region = "start", output = NULL)
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. |
a ggplot object of the coverage plot, NULL if output is set, then the plot will only be saved to location.
Other coveragePlot: coverageHeatMap
,
savePlot
, windowCoveragePlot
# 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