readWhippetPSIfiles: Read in a list of whippet .psi.gz files and format as a...

In betsig/GeneStructureTools: Tools for spliced gene structure manipulation and analysis

Description

Read in a list of whippet .psi.gz files and format as a data.frame

Usage

readWhippetPSIfiles(files, attribute = "Total_Reads", maxNA = NA)

Arguments

files	vector of *.psi.gz file names
attribute	which attribute from the PSI files to use (Total_Reads, Psi, CI_width)
maxNA	maximum number of NA values allowed before a site is removed

Value

data.frame with junction counts for all files

Author(s)

Beth Signal

See Also

Other whippet data processing: coordinates(), diffSplicingResults(), filterWhippetEvents(), formatWhippetEvents(), junctions(), readCounts(), readWhippetDIFFfiles(), readWhippetDataSet(), readWhippetJNCfiles(), whippetTranscriptChangeSummary()

Examples

whippetFiles <- list.files(system.file("extdata", "whippet_small/",
    package = "GeneStructureTools"
), full.names = TRUE)
psiFiles <- whippetFiles[grep(".psi", whippetFiles)]
whippetPSI <- readWhippetPSIfiles(psiFiles)

betsig/GeneStructureTools documentation built on March 31, 2021, 4:43 a.m.