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

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

Create and store the output of the diffExpressedVariants function in a file and in a rds object.

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).

In both cases, an rds object is saved in the output folder, that can be used to explore the results of kissDE through a Shiny application with the exploreResults 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)

aursiber/kissDE documentation built on Jan. 28, 2024, 10:01 a.m.