countReadsAnnotated: Sum up aligned reads per category of genome feature

In girafe: Genome Intervals and Read Alignments for Functional Exploration

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")

girafe documentation built on Nov. 8, 2020, 4:56 p.m.