count_reads_at_groups: A function that counts the reads at specific positions in...
In shahlab/RiboRet: Shah lab RiboRet functions

Description Usage Arguments Value

View source: R/count_reads_at_groups.R

This function is intended to use the GRanges output from find_related_positions to count the number of reads that occur in groups of positions that looked interesting across the samples but can use any GRanges object you're interested in, for example, a start codon only GFF. This function defaults to 4 threads.

1	count_reads_at_groups(bamList, gRangesToLookFor)

`bamList`	A list of bams produced by parallel_read_bams, or one cleaned of contaminating reads by remove_contam_reads.
`gRangesToLookFor`	a GRanges object. Reads corresponding to the ranges in this object will be found from each of the bam files

Returns a data frame that shows the number of reads from each file mapping within the ranges specified in gRangesToLookFor

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