writeOutputKissDE: Create and store the output of the 'diffExpressedVariants'...

In kissDE: Retrieves Condition-Specific Variants in RNA-Seq Data

Description

If a KisSplice fasta file was used as input for the analysis, writeOutputKissDE will output a tab-delimited file containing one alternative splicing event/SNV per line. The columns are: the ID of the variation, the variable part length, the counts of each variant for each condition, the adjusted p-value (FDR), the deltaPSI and a boolean indicating if the splicing event/SNV was sufficiently expressed (controled by the flagLowCountsConditions option from the diffExpressedVariants function).

If a KisSplice2RefGenome file was used as input for the analysis, this function will add five columns to the KisSplice2RefGenome file, with the following KissDE results: normalized counts, PSI computed from normalized counts, adjusted p-value, deltaPSI and a boolean indicating if the splicing event/SNV was sufficiently expressed in at least half of the conditions (controled by the flagLowCountsConditions option from the diffExpressedVariants function).

Usage

writeOutputKissDE(resDiffExprVariant, output, adjPvalMax = 1, dPSImin = 0, 
    writePSI = FALSE)

Arguments

resDiffExprVariant	a list, returned by diffExpressedVariants.
output	a character indicating the path and file name to save writeOutputKissDE output.
adjPvalMax	a double indicating the threshold for adjusted p-value. Only SNVs/splicing events with an adjusted p-value lower than this threshold will be kept in the output file.
dPSImin	a double indicating the threshold for the deltaPSI. Only SNVs/splicing events having an absolute value of deltaf/deltaPSI higher than this threshold will be kept in the output file.
writePSI	a boolean indicating if the user wants the f/PSI table to be printed (TRUE) instead of the final table (FALSE, default).

Value

None.

Examples

kissplice2refgenome_file <- system.file("extdata", 
    "output_k2rg_alt_splicing.txt", package="kissDE")
mySplicingconditions <- c("C1", "C1", "C2", "C2")
counts <- kissplice2counts(fileName=kissplice2refgenome_file, counts=2,
    pairedEnd=TRUE, k2rg=TRUE)
# res <- diffExpressedVariants(countsData=counts, 
#   conditions=mySplicingconditions)
# writeOutputKissDE(res, output="results.tsv")
# writeOutputKissDE(res, output="significants_results.tsv", 
#   adjPvalMax=0.05, dPSImin=0.1)
# writeOutputKissDE(res, output="psi_results.tsv", adjPvalMax=0.05,
#   dPSImin=0.1, writePSI=TRUE)

kissDE documentation built on Nov. 8, 2020, 5:41 p.m.