girafe (version 1.24.0)

countReadsAnnotated: 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?

Value

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

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.

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")