kissDE: Run the whole kissDE analysis

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

Run the whole kissDE analysis

Description

This function will sequentially call the kissplice2counts, diffExpressedVariants and writeOutputKissDE functions in order to run a complete kissDE analysis. It may also call the qualityControl and the exploreResults functions.

Usage

kissDE(fileName, conditions, output, counts = 2, pairedEnd = FALSE,
       order = NULL, exonicReads = TRUE, k2rg = FALSE, keep = c("All"), remove = NULL,
       pvalue = 1, filterLowCountsVariants = 10, flagLowCountsConditions = 10,
       technicalReplicates = FALSE, nbCore = 1, adjPvalMax = 1, dPSImin = 0,
       writePSI = TRUE, doQualityControl = TRUE, resultsInShiny=TRUE)

Arguments

fileName	a string indicating the path to the KisSplice (.fa) or the KisSplice2RefGenome (tab-delimited) file.
conditions	a character vector containing the experimental conditions.
output	a character indicating the path and file name to save writeOutputKissDE output.
counts	an interger (0, 1 or 2) corresponding to the KisSplice counts option used (see Details below).
pairedEnd	a logical indicating if the data is paired-end (FALSE, default). If set to TRUE, the sum of the counts from the pair of reads will be computed. It can be used along with counts option. By default, it is assumed that, in the KisSplice command line, two reads of the same pair has been inputed as following each other. If it is not the case, see option order.
order	a numeric vector indicating the actual order of the corresponding paired reads in the columns of the KisSplice output such that they can be summed. This option goes along with pairedEnd = TRUE, if the read pairs are not in the expected order (see pairedEnd option). It has as many elements as there are samples in total. For more information on this parameter, see Details in kissplice2counts.
exonicReads	a logical indicating if exonic/intronic read counts will be kept (TRUE, default) or discareded (FALSE). This option only works if counts = 2.
k2rg	a logical indicating if the input file is a KisSplice2RefGenome (TRUE) output or a KisSplice (FALSE, default) output file.
keep	a character vector listing the names of the events to be kept for the statistical test (for k2rg = TRUE, analyses all of the events by default). The test will be more sensitive the selected events. Event(s) name(s) must be part of this list: deletion, insertion, indel, IR, ES, altA, altD, altAD, alt, - (for unclassified events). For more information on this parameter, see Details in kissplice2counts.
remove	a character vector listing the names of the events to remove for the statistical test (for k2rg = TRUE, does not remove any event by default). The test will be more sensitive for the non-selected events. Event(s) name(s) must be part of this list: deletion, insertion, indel, IR, ES, altA, altD, altAD, alt, - (for unclassified events), MULTI. This option can not be used along with the keep option, unless ES is one of the events to be kept. In this case, the remove option will work on specific ES events. For more information on this parameter, see Details in kissplice2counts.
pvalue	a numerical value indicating the p-value threshold below which the events will be kept in the final data frame.
filterLowCountsVariants	a numerical value indicating the global variant count value (see Details below) below which events are filtered out in order to increase statistical power of the analysis. Both variant must have a read coverage below this value in order to remove the event. This filter is done after the normalization and the overdispersion estimation.
flagLowCountsConditions	a numerical value indicating the global condition count value (see Details below) below which we flag events as 'lowCounts' in the final data frame. At least n-1 conditions (over n conditions) must have low counts to flag the event as 'lowCounts'.
technicalReplicates	a boolean value indicating if the counts in countsData come from technical replicates only or not.
nbCore	an integer indicating the number of cores to use for the model fitting step.
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, default) along with the final table (FALSE).
doQualityControl	a boolean indicating if the user wants quality control plots to be written in the output folder (TRUE, default) or not (FALSE). See details in qualityControl.
resultsInShiny	a boolean indicating if the user wants the results to be printed in a Shiny application (TRUE, default) or not (FALSE). See details in exploreResults.

Value

None.

Examples

kissplice2refgenome_file <- system.file("extdata", 
    "output_k2rg_alt_splicing.txt", package="kissDE")
mySplicingconditions <- c("C1", "C1", "C2", "C2")
#kissDE(fileName=kissplice2refgenome_file, conditions=mySplicingconditions, 
#       output="results.tsv", counts=2, pairedEnd=TRUE, k2rg=TRUE)

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