rds: Read density of gene and bins

In chernolab/ASpli: Analysis of Alternative Splicing Using RNA-Seq

Description

Read density of gene and bins is the quotient between the number of read counts and the length of the feature. The results are appended into an ASpliCounts object that must be given as argument. The explicit calculation of read densities is usually not required because is automatically performed by readCounts function.

Usage

  rds( counts, targets )

Arguments

counts	An ASpliCounts object
targets	A data frame containing sample, bam and experimental factors columns

Value

An ASpliCounts object containing read densities of genes and bins.

Author(s)

Estefania Mancini, Andres Rabinovich, Javier Iserte, 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 )
#                          
#  # Calculates read densities
#  counts <- rds( counts, targets )

chernolab/ASpli documentation built on March 11, 2021, 12:24 a.m.