writeOutputKissDE {kissDE} | R Documentation |
diffExpressedVariants
function in a file.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).
writeOutputKissDE(resDiffExprVariant, output, adjPvalMax = 1, dPSImin = 0, writePSI = FALSE)
resDiffExprVariant |
a list, returned by
|
output |
a character indicating the path and file name to save
|
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 ( |
None.
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)