countReadsAnnotated {girafe} | R Documentation

## Sum up aligned reads per category of genome feature

### Description

A function to sum up aligned reads per category of genome feature (i.e. gene, ncRNA, etc.).

### Usage

    countReadsAnnotated(GI, M, typeColumn="type", fractionGI=0.7,
                        mem.friendly=FALSE, showAllTypes=FALSE)

### Arguments

`GI` | object of class `AlignedGenomeIntervals`
`M` | Annotation object of class `Genome_intervals_stranded` or `Genome_intervals`; describes the genomic coordinates of annotated genome features, such as genes, miRNAs, etc.
`typeColumn` | string; which column of the annotation object `M` describes the type of the genome feature
`fractionGI` | which fraction of the intervals in object `GI` are required to ovelap with a feature in `M` in order to be considered to correspond to that feature.
`mem.friendly` | logical; should a version which requires less memory but takes a bit longer be used
`showAllTypes` | logical; should a table of genome feature types in `M` be displayed?

### Details

The read counts are summed up over each type of genome feature, and the read counts are normalised by their number of genomic matches. For example if a read has two matches in the genome, but only one inside a miRNA, it would count 0.5 for miRNAs.

### Value

A named numeric vector which gives the summed read counts for each supplied type of genome feature.

### Author(s)

J Toedling

### Examples

      A <- AlignedGenomeIntervals(
               start=c(1,8,14,20), end=c(5,15,19,25),
               chromosome=rep("chr1", each=4),
               strand=c("+","+","+","+"),
               sequence=c("ACATT","TATCGGAC","TCGGACT","GTAACG"),
               reads=c(7L, 2L, 4L, 5L) )
      M2 <- new("Genome_intervals_stranded",
                rbind(c(2,6), c(1,15), c(20,30)),
                closed = matrix(TRUE, ncol=2, nrow=3),
                annotation = data.frame(
                  seq_name= factor(rep("chr1", 3)),
                  inter_base= logical(3),
                  strand=factor(rep("+", 3), levels=c("+","-")),
                  alias=c("miRNA1","gene1","tRNA1"),
                  type=c("miRNA","gene","tRNA")) )
      if (interactive()){
         grid.newpage()
         plot(A, M2, chr="chr1", start=0, end=35,
              nameColum="alias", show="plus")
      }
      countReadsAnnotated(A, M2, typeColumn="type")

[Package girafe version 1.38.0 Index]