generateDistn: Generate theoretical GC content distributions
In mikelove/fastqcTheoreticalGC: Generate theoretical GC content

Description Usage Arguments Value References

This function generates random simulated reads from either provided seqs (best for RNA-seq) or from a genome (best for DNA-seq). The GC content of these reads is then tabulated to produce a distribution file which can be read by MultiQC to be displayed on top of the FASTQC GC content module. Either seqs or genome is required, and only one can be specified. Specifying genome requires also specifying nchrom.

1 2	generateDistn(seqs, genome, nchrom, file = "fastqc_theoretical_gc.txt", n = 1e+06, bp = 100, wts = 1, name = "")

`seqs`	a DNAStringSet of the sequences to simulate read from. E.g. for RNA-seq, the transcripts, which can be generated with `extractTranscriptSeqs` from the GenomicFeatures package. See the example script located in `inst/script/human_mouse.R`
`genome`	a BSgenome object. See the example script located in `inst/script/human_mouse.R`
`nchrom`	the number of chromosomes from the genome to simulate reads from
`file`	the path of the file to write out
`n`	the number of reads to simulate
`bp`	the basepair of the reads
`wts`	optional weights to go along with the `seqs` or the chromosomes in `genome`, e.g. to represent more realistic expression of transcripts
`name`	the name to be printed at the top of the file