propPhred {seqTools} | R Documentation |
The propPhred
function returns a named vector
with relative Phred content for all contained lanes.
propPhred(object, greater = 30, less = 93)
object |
|
greater |
|
less |
|
The greater
and less
arguments must be numeric, have
length 1 and be >0 and < 94. greater
must be less than less
.
With the default settings the reported proportions should be >50 % for
all lanes in order to be acceptable (see 't Hoen et. al.).
Numeric.
Wolfgang Kaisers
't Hoen et.al Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories Nature Biotechnology 2013 Vol. 31 1015 - 1022 (doi:10.1038/nbt.2702)
basedir <- system.file("extdata", package="seqTools") setwd(basedir) # fq <- fastqq(c("g4_l101_n100.fq.gz", "g5_l101_n100.fq.gz"), k=4, probeLabel=c("g4", "g5")) # Proportion of phred Values >30 propPhred(fq) # Proportion of phred Values >10 and < 30 propPhred(fq, greater=10, less=30)