ExonQuant: Count exon inclusion and exclusion according to grouping...

In noush-joglekar/scisorseqr: Processes long reads for differential isoform analysis

Count exon inclusion and exclusion according to grouping factor

Description

This function groups reads by either the celltype or cell-barcode to count inclusion and exclusion of exons. Inputs to this function are based on previous preprocessing steps

For ONT data we recomment https://github.com/ablab/IsoQuant which allows for non-exact splice-site matching

Usage

ExonQuant(
  allInfoFile = "LongReadInfo/AllInfo_IncompleteReads.gz",
  groupingFactor = "Celltype",
  threshold = 10,
  numThreads = 4
)

Arguments

allInfoFile	file containing barcode, celltype, and exon information per read. Defaults to output of the InfoPerLongRead function
groupingFactor	"Celltype" or "Barcode" to group reads by for counting inclusion levels. Defaults to Celltype
threshold	minimum number of reads per grouping factor in order to consider that exon to be sufficiently expressed. Defaults to 10
threads	number of threads to parallelize the function. Defaults to 4

Value

ExonQuantOutput/InclusionExclusionCounts.tsv

See Also

MapAndFilter

InfoPerLongRead

https://github.com/ablab/IsoQuant

noush-joglekar/scisorseqr documentation built on March 18, 2023, 8:06 p.m.