splitting.data-methods: Split data into subsites

In pievos101/PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses

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 signature '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

Details

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

Value

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

Examples

# 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 

pievos101/PopGenome documentation built on Feb. 24, 2023, 7:11 a.m.