find_related_positions: Finds genomic positions that have many reads mapping to them.

In shahlab/RiboRet: Shah lab RiboRet functions

Description

This function helps the user find positions that have many reads mapping to them across all their samples under the logic that positions with many reads mapping to them in at least one sample (though not necessarily others) could be important.

Usage

find_related_positions(bamDf, maxDiff, gffLoc)

Arguments

bamDf	A data frame produced by the tally_reads function
maxDiff	an integer, the maximum distance in number of bases to consider something as "close". If a read occurs at position 1 and another at position 4, these reads will be in the same "group" if maxDiff >= 3 but in separate groups if maxDist <= 2
gffLoc	the location of a gff

Value

a GRanges object that shows positions that have many reads at them across all samples.

shahlab/RiboRet documentation built on Dec. 23, 2021, 1:17 a.m.