countReadsAnnotated {girafe} | R Documentation |
A function to sum up aligned reads per category of genome feature (i.e. gene, ncRNA, etc.).
countReadsAnnotated(GI, M, typeColumn="type", fractionGI=0.7, mem.friendly=FALSE, showAllTypes=FALSE)
GI |
object of class |
M |
Annotation object of class |
typeColumn |
string; which column of the annotation object
|
fractionGI |
which fraction of the intervals in object |
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
|
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.
A named numeric vector which gives the summed read counts for each supplied type of genome feature.
J Toedling
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")