README.md

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

distIUPAC

Installation

R specific installation prerequisites

First install Biostrings package from bioconductor.

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Biostrings")

Second install additional packages from cran CRAN.

In most cases you need to first install the following system-wide packages to be able to compile the R dependencies.

Ubuntu/Debian

sudo apt-get install libcurl4-openssl-dev libssl-dev libxml2-dev

CentOS

sudo yum install libcurl-devel openssl-devel libxml2-devel

• devtools
• knitr
• Rcpp
• RcppThread
• ape
• foreach
• doMC

install.packages("devtools")
install.packages("Rcpp")
install.packages("RcppThread")
install.packages("ape")
install.packages("foreach")
install.packages("doMC")
install.packages("magrittr")
install.packages("rlist")

Third install distIUPAC package from github or gwdg gitlab using the devtools package.

library(devtools)
install_github("kullrich/distIUPAC", build_vignettes = TRUE, dependencies = FALSE)
#install_git("https://gwdg.gitlab.de/evolgen/distIUPAC.git", build_vignettes = TRUE, dependencies = FALSE)

Vignettes

These vignettes introduce distIUPAC

• 00. Intro
• 01. bam2IUPAC: fastq + reference >>> reference mapped bam + angsd >>> iupac fasta
• 02. distStats+ABBA-BABA: population distanceStats per sliding-window: iupac fasta + pop info >>> dStats
• 03. getTrees: genrate twisst input: iupac fasta >>> twisst trees
• 04. getTreemix: genrate treemix input: iupac fasta >>> treemix
• 05. distFeatures: using GFF3/GTF features: iupac fasta + GTF >>> feature specific distances

Quick-guide

library(distIUPAC)

#browse vignettes
browseVignettes("distIUPAC")

#load IUPAC encoded nucleotide sequences with Biostrings
#change path to your input file
#lada fasta file
input.fasta <- readDNAStringSet(paste0(find.package("distIUPAC"),"/data/seqIUPAC.fasta.gz"))


#use example sequences
data("MySequences", package = "distIUPAC")
MySequences

#consider only a subset of all sequences
CAS.pos <- 5:34

#get IUPAC distances using a pre-defined distance matrix
CAS.distIUPAC <- distIUPAC(as.character(MySequences[CAS.pos]))

#get pairwise IUPAC distances as distance matrix
as.dist(CAS.distIUPAC$distIUPAC)

#get pairwise used sites as distance matrix
as.dist(CAS.distIUPAC$sitesUsed)

#plot bionj tree based on IUPAC distances
plot(bionj(as.dist(CAS.distIUPAC$distIUPAC)))

#get IUPAC distance using your own distance matrix
MyScoreMatrix <- scoreMatrix()
MyScoreMatrix["C","Y"] <- 1.0
distIUPACmatrix(as.character(MySequences[CAS.pos]), MyScoreMatrix)

#get mean IUPAC distances using a pre-defined distance matrix on sliding windows (xStats)
xStats(MySequences, x.pos=CAS.pos)

#get mean IUPAC distances using a pre-defined distance matrix on sliding windows using multiple threads (xStats)
xStats(MySequences[CAS.pos], threads = 4)

#get dXY calculations for three populations ((P1:i,P2:x),P3:y) on sliding windows and the (xyiStats)
AFG.pos<-82:87
SPRE.pos<-106:113
xyiStats(MySequences, x.pos=AFG.pos, y.pos=SPRE.pos, i.pos=CAS.pos, threads = 4)

#calculate ABBA-BABA statistics for four-taxon scenario (((P1:i,P2:x),P3:y),P4:o)
APO.pos<-1
xyiStats(MySequences, x.pos=AFG.pos, y.pos=SPRE.pos, i.pos=CAS.pos, o.pos=APO.pos threads = 4, do.ABBA = TRUE)

#get bi-allelic sites for population
CAS.biSites<-biSites(MySequences, x.pos = CAS.pos)
as.matrix(MySequences[CAS.pos])[,head(CAS.biSites)]

Todo

• add mask file for sliding window calculations

License

MIT (see LICENSE)

Bug reports

Please report any errors or requests regarding distIUPAC to Kristian Ullrich ([e-mail])

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