PopGenome (version 2.7.2)

splitting.data-methods: Split data into subsites

Description

This generic function splits the data into subsites, if GFF/GTF information is present or if positions are defined accordingly.

Usage

# S4 method for GENOME
splitting.data(object,subsites=FALSE,positions=FALSE,type=1,
          whole.data=TRUE)

Arguments

object

an object of class "GENOME"

positions

list of positions

subsites

"exon": SNPs in exon regions. "intron": SNPs in intron regions. "coding": SNPs in coding regions (CDS). "utr": SNPs in UTR regions. "gene": SNPs in genes.

type

1: SNP positions 2: Genome positions

whole.data

Scan the whole data by concatenating the regions. If FALSE, the regions are scanned seperately

Value

The return value is a modified object of class "GENOME".

Details

Note, if whole.data=FALSE data with n.biallelic.sites==0 should be removed.

Examples

# NOT RUN {
# GENOME.class <- readData("\home\Alignments")
# GENOME.class
# GENOME.class.split <- splitting.data(GENOME.class,subsites="exon")
# [e-mail]
# GENOME.class.split <- splitting.data(GENOME.class,positions=list(1:7,8:12))
# GENOME.class.split <- splitting.data(GENOME.class,
# positions=list(2000:3000,12000:13000),type=2)
# GENOME.class.split 

# }