propPhred: propPhred: Lane specific proportion of reads in a specified...
In seqTools: Analysis of nucleotide, sequence and quality content on fastq files

Description Usage Arguments Details Value Author(s) References Examples

The propPhred function returns a named vector with relative Phred content for all contained lanes.

1	propPhred(object, greater = 30, less = 93)

object

Fastqq: Object which contains collected values from FASTQ files.

greater

numeric: Limits the counted proportion of phred to values which are greater than the given value (default: 30).

less

numeric: Limits the counted proportion of phred to values which are less than the given value (default: 93).

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)