rbamtools (version 2.16.17)

groupRatio: Calculates group-wise ratios of alignment depth (AD)

Description

groupRatio takes a bamRange and returns a data.frame (128 rows, number of columns=length of the longest sequence in range). groupRatio counts occurrences for every sequence position (column) and every phred value (row). getQualQuantiles takes a bamReader and a vector of quantiles (must be between 0 and 1) and returns a data.frame. The data.frame contains one row for each quantile and also as many columns as the maximum sequence length. plotQualQuant plots the values for quanties 0.1,0.25,0.5,0.75 and 0.9.

Usage

groupRatio(object, lim=1.2, cut=0, order=NULL, f=mean)

Arguments

object

exonLoessModel

lim

numeric. Limit ratio. Must be > 1. The function returns the fraction of genetic position where AD-ratio between groups is > lim or the fraction of positions where AD-Ratio is < 1/lim (i.e the larger ratio).

cut

numeric. When >0 , the function uses cutFlatAlignDepth for cutting out low alignment depth regions before calculating. alignment depth ratio.

order

numeric. When given, the function reorders the sample groups. Can be used to provide ascending (or descending) group ordering, e.g. group1 < group2 < group3.

f

function. Function for calculation of group accumulates. Defaults to mean. Alternatively median may also be used.

Value

numeric

Details

The size of the returned value (abs(groupRatio)) indicates on which proportion of the genetic region, AD ratio between subsequent groups exceeds the given limit. For lim=1.1, group1<group2<group3, a returned value of 0.8 says that the AD ratios group2:group1 and group3:group2 are at least 1.1 (> 1) on 80 percent of the contained genomic positions. Negative values say that the relation is group1>group2>group3. This allows discrimination of up- and down-regulated genes.

Examples

# NOT RUN {
## - - - - - - - - - - - - - - - - - - - - - - ##
# Construct sampleBamFiles object
bam <- system.file("extdata", "accepted_hits.bam", package="rbamtools")
bs <- sampleBamFiles(1)
bamFiles(bs) <- bam
sampleLabels(bs) <- "s1"
sampleGroups(bs) <- "g1"
checkBamFiles(bs)
nAligns(bs) <- bamCountAll(bs)
bs
## - - - - - - - - - - - - - - - - - - - - - - ##
# Construct geneModel object
library(refGenome)
ucfile <- system.file("extdata", "hs.ucsc.small.RData", package="refGenome")
uc <- loadGenome(ucfile)
gt <- getGeneTable(uc)
gene_id <- as.character(gt$gene_id[1])
gm <- geneModel(uc, gene_id)
## - - - - - - - - - - - - - - - - - - - - - - ##
# Construct geneAlignDepth object
gad <- geneAlignDepth(bs, gm)
## - - - - - - - - - - - - - - - - - - - - - - ##
# Extract exonLoessModel object
ead <- exonAlignDepth(gad, ratioLim=5, infVal=1000)
elm <- exonLoessModel(ead)
celm <- cutFlatAlignDepth(elm, ratio=0.1)
groupRatio(celm, lim=1.2, cut=0, order=1)
# }