nx: Calcuration of NX and LX from genome sequence.

Description Usage Arguments Examples

View source: R/nx.R

Description

Calculation of NX and LX from genomic sequence in fasta format. If the genomic sequence is pseudo chromosomes, L50 is no needed.

Usage

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nx(in_f, genome, asmbl)

Arguments

in_f

The input file path with fasta format, or DNAStringSet object from Biostrings package.

genome

numeric: genome size. The default is NULL. The genome size is calculated from the sum of the widths of the input fasta files.

asmbl

character: assembly name. The N50 is compared to the previous assembly.

Examples

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## Not run: 
fas <- "~/db/genome/CHOK1GS_HDv1/CHOK1GS_HDv1.dna.toplevel.fa.gz"
nxdat <- rskoseq::nx(in_f = fas, asmbl = "CHOK1GS_HDv1")
plot(x = nxdat$NGX, y = nxdat$Mbp, xlab = "NX", ylab = "contig length(Mbp)")
abline(v = 50, lty = 3)

## End(Not run)

shkonishi/rskoseq documentation built on April 18, 2021, 3:50 p.m.