DiffSplicingAnalysis: Perform differential splicing analysis

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

Perform differential splicing analysis

Description

This function allows you to test alternative splicing differences between any two groups based on the full splice-form, exons, the transcription start site (TSS) or end site (polyA).

Usage

DiffSplicingAnalysis('config',10,25,'Exon',is.hier=FALSE)

Arguments

configFile	File in a .tsv format with four columns specifying the comparisons to be made
numIsoforms	Cap on the number of sites to test per gene. Defaults to 10
minNumReads	Parameter to filter out lowly expressed genes. Defaults to 25
typeOfTest	Exon, TSS, PolyA or Isoform test conducted depending on input. Defaults to Iso
numThreads	number of parallel processes for the differential testing. Defaults to 10
is.hier	OPTIONAL logical indicating hierarchical structure
region1	string containing comparison1 for parsing if is.hier is TRUE
region2	string containing comparison2 for parsing if is.hier is TRUE
yamlFile	.yaml file indicating hierarchical structure

Value

Output folder with results for each line of config file, i.e. for each set of comparisons

Result file with gene, uncorrected pval, deltaPI, FDR

handy .Robj per comparison to import if need be

file with significantly differentially spliced genes

file with numbers per gene and isoform tested in each group

See Also

IsoQuant

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