AsDiscover {ASpli} | R Documentation

## Report PSI and PIR using experimental junctions

### Description

Given a bin, it is possible to calculate PSI/PIR metric using junctions to estimate changes in the use of it along different conditions. PSI or PIR metric is calculated for each bin and experimental condition. The selection of which metric is used is based on the kind of splicing event associated with each bin.

### Usage

     AsDiscover( counts, targets, features, bam, readLength, threshold , cores )

### Arguments

`counts` | An object of class ASpliCounts.
`targets` | A dataframe containing sample, bam and experimental factors as columns and samples as rows.
`features` | An object of class ASpliFeatures.
`bam` | A list with BAM files contents.
`readLength` | Read length of sequenced read. Default 100L
`threshold` | Minimum number of reads supporting junctions. Default=5
`cores` | Number of processing cores to use

### Value

An object of class ASpliAS

`irPIR` | reports: event, e1i counts (J1), ie1 counts (J2), j_within (J3), PIR by condition. J1, J2, J3 sum of junctions (J1, J2, J3) by condition.
`altPSI` | reports: event, J1 (start), J2 (end), J3 (exclusion), PSI. J1, J2, J3 sum of junctions (J1, J2, J3) by condition.
`esPSI` | reports: event, J1 (start), J2 (end), J3 (exclusion), PSI. J1, J2, J3 sum of junctions (J1, J2, J3) by condition.
`junctionsPIR` | PIR metric for each experimental junction using e1i and ie2 counts. Exclusion junction is the junction itself. This output helps to discover new introns as well as new retention events.
`junctionsPSI` | Given a junction, it is possible to analyze if it shares start, end or both with another junction. If so, is because there is more than one way for/of splicing. Ratio between them along samples is reported.

### Author(s)

Estefania Mancini, Marcelo Yanovsky and Ariel Chernomoretz

### See Also

Accesors: `irPIR`, `altPSI`, `esPSI`, `junctionsPIR`, `junctionsPSI`

Export: `writeAS`

### Examples

      # Create a transcript DB from gff/gtf annotation file.
      # Warnings in this examples can be ignored.
      library(GenomicFeatures)
      genomeTxDb <- makeTxDbFromGFF( system.file('extdata','genes.mini.gtf',
                                     package="ASpli") )

      # Create an ASpliFeatures object from TxDb
      features <- binGenome( genomeTxDb )

      # Define bam files, sample names and experimental factors for targets.
      bamFileNames <- c( "A_C_0.bam", "A_C_1.bam", "A_C_2.bam",
                         "A_D_0.bam", "A_D_1.bam", "A_D_2.bam" )
      targets <- data.frame(
                   row.names = paste0('Sample_',c(1:6)),
                   bam = system.file( 'extdata', bamFileNames, package="ASpli" ),
                   factor1 = c( 'C','C','C','D','D','D') )

      # Load reads from bam files
      bams <- loadBAM( targets )

      # Read counts from bam files
      counts   <- readCounts( features, bams, targets, cores = 1, readLength = 100,
                              maxISize = 50000 )

      # Calculate differential usage of genes, bins and junctions
      du       <- DUreport( counts, targets )
      du       <- junctionDUreport( counts, targets, appendTo = du)

      # Calculate PSI / PIR for bins and junction.
      as       <- AsDiscover( counts, targets, features, bams, readLength = 100,
                              threshold = 5, cores = 1 )

      writeAS( as = as, output.dir = "only_as" )

[Package ASpli version 1.14.0 Index]