rds {ASpli} | R Documentation

## Read density of gene and bins

### 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, 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 )

[Package ASpli version 1.12.0 Index]