splitIn3Tx {ORFik} | R Documentation |
The 3 parts of transcripts are the leaders, the cds' and trailers. Per transcript part, bin them all to windowSize (default 100), and make a data.table, rows are positions, useful for plotting with ORFik and ggplot2.
splitIn3Tx( leaders, cds, trailers, reads, windowSize = 100, fraction = "1", weight = "score", is.sorted = FALSE, BPPARAM = BiocParallel::SerialParam() )
leaders |
a |
cds |
a |
trailers |
a |
reads |
GRanges or GAlignment of reads |
windowSize |
an integer (100), size of windows (columns) |
fraction |
a character (1), info on reads (which read length, or which type (RNA seq)) (row names) |
weight |
(default: 'score'), if defined a character name of valid meta column in subject. GRanges("chr1", 1, "+", score = 5), would mean score column tells that this alignment region was found 5 times. ORFik .bedo files, contains a score column like this. As do CAGEr CAGE files and many other package formats. You can also assign a score column manually. |
is.sorted |
logical (FALSE), is grl sorted. That is + strand groups in increasing ranges (1,2,3), and - strand groups in decreasing ranges (3,2,1) |
BPPARAM |
how many cores/threads to use? default: bpparam() |
a data.table with columns position, score