getQualDf takes a
bamRange and returns a data.frame
(128 rows, number of columns=length of the longest sequence in range).
getQualDf 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.
logical. When TRUE each column is divided by its sum.
The column sums are added as names attribute
Phred values are truncated by 127 (the maximum which can be represented by ASCII values). The function runs down each colum (sequence position) and returns the row index where the quantile exceeds the cumlated column values.
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# A) Read bamRange bam<-system.file("extdata","accepted_hits.bam",package="rbamtools") reader<-bamReader(bam,idx=TRUE) coords<-as.integer(c(0,0,249250621)) range<-bamRange(reader,coords) bamClose(reader) # B) getQualDf qdf<-getQualDf(range) qdf[32:38,1:15] qdr<-getQualDf(range,prob=TRUE) # C) getQualQuantiles quantiles<-c(0.1,0.25,0.5,0.75,0.9) qt<-getQualQuantiles(range,quantiles) # D) Plot plotQualQuant(range)
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