process_spikes: QC, QA, and processing for a new spike database

In trichelab/spiky: Spike-in calibration for cell-free MeDIP

QC, QA, and processing for a new spike database

Description

Sequence feature verification: never trust anyone, least of all yourself.

Usage

process_spikes(fasta, methylated = 0, ...)

Arguments

fasta	fasta file (or GRanges or DataFrame) w/spike sequences
methylated	whether CpGs in each are methylated (0 or 1, default 0)
...	additional arguments, e.g. kernels (currently unused)

Details

GCfrac is the GC content of spikes as a proportion instead of a percent. OECpG is (observed/expected) CpGs (expectation is 25% of GC dinucleotides).

Value

         a DataFrame suitable for downstream processing

See Also

kmers

Examples

data(spike)
spikes <- system.file("extdata", "spikes.fa", package="spiky", mustWork=TRUE)
spikemeth <- spike$methylated
process_spikes(spikes, spikemeth)

data(phage)
phages <- system.file("extdata", "phages.fa", package="spiky", mustWork=TRUE)
identical(process_spikes(phage), phage)
identical(phage, process_spikes(phage))

data(genbank_mito)
(mt <- process_spikes(genbank_mito)) # see also genbank_mito.R
gb_mito <- system.file("extdata", "genbank_mito.R", package="spiky")

trichelab/spiky documentation built on Sept. 17, 2022, 8:44 a.m.