kissplice2counts: Conversion of 'KisSplice' or 'KisSplice2RefGenome' outputs
In kissDE: Retrieves Condition-Specific Variants in RNA-Seq Data

Description Usage Arguments Details Value Examples

View source: R/kissplice2counts.R

Function that converts KisSplice (.fa) output or KisSplice2RefGenome (tab-delimited) output to a counts data frame that can be used by other functions of the KissDE package.

1 2	kissplice2counts(fileName, counts = 2, pairedEnd = FALSE, order = NULL, exonicReads = TRUE, k2rg = FALSE, keep = c("All"), remove = NULL)

`fileName`	a string indicating the path to the `KisSplice` (`.fa`) or the `KisSplice2RefGenome` (tab-delimited) file.
`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 below.
`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, IR, ES, altA, altD, altAD, alt, unclassified. For more information on this parameter, see Details below.
`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, IR, ES, altA, altD, altAD, alt, unclassified, 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 below.

The counts parameter:

By default, as in KisSplice, the counts option is set to 0, assuming there is no special counting option. Below, an example of the upper path counts format output by KisSplice when counts is set to 2:

|AS1_0|SB1_0|S1_0|ASSB1_0|AS2_27|SB2_41|S2_0|ASSB2_21|

AS3_0|SB3_0|S3_0|ASSB3_0|AS4_7|SB4_8|S4_0|ASSB4_2.

In a regular KisSplice output (counts = 0), it would be:

|C1_0|C2_47|C3_1|C4_13 (with 47 = 27+41+0-21 and 13 = 7+8+0-2)

The order parameter:

If the reads corresponding to a paired-end fragments have not been passed to Kissplice next to each other, the order needs to be explicitly given to the kissplice2counts function. For instance, if there are two paired-end samples and if the input in Kissplice has been: -r sample1_readPair1.fa -r sample2_readPair1.fa -r sample1_readPair2.fa -r sample2_readPair2.fa, the input is not organised with the reads of one pair next to each other. The vector order to give would be order = c(1, 2, 1, 2).

The keep and remove parameters:

The options keep and remove allow the user to select the type of alternative splicing events from KisSplice2RefGenome that have to be analysed. To work only with intron retention events, the vector should be: keep = c("IR"). To work on all events except insertions and deletions, the vector should be remove = c("insertion","deletion"). To work specifically on single exon skipping (ES) events (only one exon can be included or excluded), both keep and remove options must be used. The keep option should be set to c("ES") and the remove option should be set to c("alt","altA","altD","altAD","MULTI").

kissplice2counts returns a list of 4 objects:

`countsEvents`	a data frame containing several columns: a first column (`events.names`) with the name of the event based on `KisSplice` notation, a second one (`events.length`) containing the length of the event, and the remaining others columns (`counts1` to `countsN`) with the counts corresponding to the replicates of the conditions.
`psiInfo`	a data frame containing information to compute the PSI values. This data frame is used only when `counts` is different from 0.
`exonicReadsInfo`	a logical indicating if `exonicReads` are used.
`k2rgFile`	a string containing the `KisSplice2RefGenome` path and file name. It is equal to NULL if the input file comes from KisSplice.

Only countsEvents is shown when kissplice2counts output is printed.

fpath <- system.file("extdata", "output_kissplice_SNV.fa", package="kissDE")
mySNVcounts <- kissplice2counts(fpath, counts = 0, pairedEnd=TRUE)
names(mySNVcounts)
str(mySNVcounts)
head(mySNVcounts$countsEvents)