readCounts {ASpli}R Documentation

Summarize read overlaps

Description

Summarize read overlaps against all feature levels

Usage

  readCounts( features, bam, targets, cores = 1, readLength,
                 maxISize, minAnchor = 10)

Arguments

features

An object of class ASpliFeatures. It is a list of GRanges at gene, bin and junction level

bam

List of GAlignments objects corresponding to bam files of samples.

targets

A dataframe containing sample, bam and experimental factors columns

readLength

Read length of sequenced library. It is used for compute E1I and IE2 read summarization

maxISize

maximum intron expected size. Junctions longer than this size will be dicarded

cores

Number of cores to use. Default is 1

minAnchor

Minimum percentage of read that should be aligned to an exon-intron boundary

Value

An object of class ASpliCounts. Each slot is a dataframe containing features metadata and read counts. Summarization is reported at gene, bin, junction and intron flanking regions (E1I, IE2).

Author(s)

Estefania Mancini, Javier Iserte, Marcelo Yanovsky, Ariel Chernomoretz

See Also

Accesors: countsg, countsb, countsj, countse1i, countsie2, rdsg, rdsb, Export: writeCounts

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 )
  # Export data
  writeCounts( counts, output.dir = "only_counts" )
  

[Package ASpli version 1.8.1 Index]