tmpSEQsw: tmpSEQsw

In kullrich/distIUPAC: calculates IUPAC distances on Biostrings DNAStringSet and BStringSet objects

Description

This function returns tmpSEQ Biostrings DNAStringSet objects as sliding windows which can be used to parse to further functions

Usage

tmpSEQsw(dna, FUN = NULL, chr.name = "chr", wlen = 25000,
  wjump = 25000, start.by = 1, end.by = NULL, wtype = "bp",
  global.deletion = TRUE, threads = 1, pB = TRUE)

Arguments

dna	DNAStringSet
FUN	the function to be applied [default: NULL] see e.g. dist.xStats, dist.xyStats, dist.xyoStats, dist.xyioStats
chr.name	chromosome name [default: "chr"]
wlen	sliding windows length [default: 25000]
wjump	sliding windows jump [default: 25000]
start.by	optional start position [default: 1]
end.by	optional end position [default: NULL] take width of DNAStringSet
wtype	sliding windows type to use bp, biSites or triSites [default: "bp"]
global.deletion	a logical indicating whether to delete the sites with missing data in a global or pairwise way (default is to delete in a global way) [default: TRUE]
threads	number of parallel threads to process windows [default: 1]
pB	specifies if progress should be shown as a progress bar [default: TRUE]

Author(s)

Kristian K Ullrich

See Also

distIUPAC, dist.dna

Examples

data("MySequences", package="distIUPAC")
CAS.pos<-5:34
CAS.tmpSEQsw<-tmpSEQsw(MySequences[CAS.pos])
##xStats
CAS.xStats<-tmpSEQsw(MySequences[CAS.pos], FUN=dist.xStats)
##multiple threads to process windows
CAS.xStats<-tmpSEQsw(MySequences[CAS.pos], threads=2)
##multiple cores to process pairwise distance calculation
CAS.xStats<-tmpSEQsw(MySequences[CAS.pos], FUN=function(x) {dist.xStats(x, ncores=2)})
##disbale global deletion
CAS.pairwiseDeletion.xStats<-tmpSEQsw(MySequences[CAS.pos],
global.deletion=FALSE, FUN=function(x) {dist.xStats(x, ncores=2)})
##using K80 distance from ape package
tmpSEQsw(MySequences[CAS.pos], FUN=function(x) {dist.xStats(x, dist="K80")})

kullrich/distIUPAC documentation built on Jan. 9, 2020, 2:50 p.m.