add.gc: Extract GC via contig FASTA file and incorporate into len-cov...

In rbhwilliams/newblerCG: Making use of the Newbler 454ContigGraph file

Description

Extract GC via contig FASTA file and incorporate into len-cov data.frame

Usage

add.gc(contigSummData, fastaFile = "454LargeContigs.fna")

Arguments

contigSummData	is a data.frame (returned from the function extract.contig.data)
fastaFile	is a FASTA file containing the DNA sequences for the contigs in the assembly

Value

A data.frame containing three columns (contig /cov/erage, contig /len/ength and contig /GC/-content). Row names are contig identifiers. Returns results for the common set of contigs between contigSummData and 454LargeContigs.fna.

Examples

## Not run: a<-extract.contig.data()
## Not run: a1<-add.gc(a,"454LargeContigs.fna")

rbhwilliams/newblerCG documentation built on May 27, 2019, 3 a.m.