distIUPACsw: distIUPACsw

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

Description

This function calculates IUPAC distances on Biostrings DNAStringSet objects on sliding windows which can be used to parse to further functions. By default, literal distances are used to calculate pairwise-distances.

Usage

distIUPACsw(dna, FUN = NULL, chr.name = "chr", wlen = 25000,
  wjump = 25000, start.by = 1, end.by = NULL, wtype = "bp",
  dist = "IUPAC", score.matrix = NULL, global.deletion = TRUE,
  threads = 1, ncores = 1, pB = TRUE)

Arguments

dna	DNAStringSet
FUN	the function to be applied [default: NULL] see e.g. dist.xStats, dist.xyStats, dist.xyoStats
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"]
dist	distance to use [default: IUPAC] or choose one model as in dist.dna [default: "IUPAC"]
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]
ncores	number of parallel cores to process pairwise distance calculation [default: 1]
pB	specifies if progress should be shown as a progress bar [default: TRUE]

Author(s)

Kristian K Ullrich

References

Chang, P. L., Kopania, E., Keeble, S., Sarver, B. A., Larson, E., Orth, A., ... & Dean, M. D. (2017). Whole exome sequencing of wild-derived inbred strains of mice improves power to link phenotype and genotype. Mammalian genome, 28(9-10), 416-425.

See Also

distIUPAC, dist.dna, scoreMatrix

Examples

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

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