Subset ASpli objects {ASpli} | R Documentation

## Subset ASpli objects

### Description

ASpli provides utility functions to easy subset ASpliCounts objects, ASpliAS objects, targets data frame and lists GAlignments generated with loadBAM function. The subset can be done selecting some of the experimental conditions or samples names ( but not both ).

### Usage

      subset( x, ... )
      subsetBams( x, targets, select )
      subsetTargets( targets, select, removeRedundantExpFactors )

### Arguments

`x` | An ASpliCount or ASpliAS object for subset function, or list of GAlignments for subsetrBams function.
`targets` | A dataframe containing sample, bam and experimental factor columns.
`select` | A character vector specifying the conditions or samples to be kept after subset operation. It's assumed that condition names are different from sample names.
`removeRedundantExpFactors` | When sub-setting the targets data frame, one or more experimental factors can have only one value. If this argument is TRUE those experimental factors are absent in the resulting target data frame.
`...` | Subsetting ASpliCounts and ASpliAS objects sub subset method requires a targets argument and a select argument with the same specifications that the arguments with the same name in subsetBams and subsetTargets functions

### Value

A data frame similar to x ( or targets for subsetTargets) with only the containing only the selected elements.

### Author(s)

Estefania Mancini, Marcelo Yanovsky, Ariel Chernomoretz

### 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 )

      # Create ASpliAS object
      as       <- AsDiscover( counts, targets, features, bams, readLength = 100,
                              threshold = 5, cores = 1 )

      # Define selection
      select <- c('Sample_1', 'Sample_2', 'Sample_4', 'Sample_5')

      # Subset target
      targets2 <- subsetTargets( targets, select )

      # Subset bams
      bams2 <- subsetBams( bams, targets, select )

      # Subset ASpliCounts object
      counts2 <- subset( counts, targets, select )

      # Subset ASpliAS object
      as2 <- subset( as, targets, select )

[Package ASpli version 1.14.0 Index]