filterCage: Filter peak of cage-data by value

In ORFik: Open Reading Frames in Genomics

Description

Filter peak of cage-data by value

Usage

filterCage(cage, filterValue = 1, fiveUTRs = NULL, preCleanup = TRUE)

Arguments

cage	Either a filePath for the CageSeq file as .bed .bam or .wig, with possible compressions (".gzip", ".gz", ".bgz"), or already loaded CageSeq peak data as GRanges or GAlignment. NOTE: If it is a .bam file, it will add a score column by running: convertToOneBasedRanges(cage, method = "5prime", addScoreColumn = TRUE) The score column is then number of replicates of read, if score column is something else, like read length, set the score column to NULL first.
filterValue	The minimum number of reads on cage position, for it to be counted as possible new tss. (represented in score column in CageSeq data) If you already filtered, set it to 0.
fiveUTRs	a GRangesList (NULL), if added will filter out cage reads by these following rules: all reads in region (-5:-1, 1:5) for each tss will be removed, removes noise.
preCleanup	logical (TRUE), if TRUE, remove all reads in region (-5:-1, 1:5) of all original tss in leaders. This is to keep original TSS if it is only +/- 5 bases from the original.

Value

the filtered Granges object

ORFik documentation built on March 27, 2021, 6 p.m.