# groupRatio: Calculates group-wise ratios of alignment depth (AD) In rbamtools: Read and Write BAM (Binary Alignment) Files

## 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

 `1` ```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.

## 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.

numeric

Wolfgang Kaisers

## Examples

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27``` ```## - - - - - - - - - - - - - - - - - - - - - - ## # 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) ```

rbamtools documentation built on May 30, 2017, 3:26 a.m.