hapFabia (version 1.14.0)

identifyDuplicates: Identify duplicates of IBD segments

Description

identifyDuplicates: R implementation of identifyDuplicates.

IBD segments that are similar to each other are identified. This function is in combination with split_sparse_matrix whith splits a chromosome in overlapping intervals. These intervals are analyzed by iterateIntervals for IBD segments. Now, these IBD segments are checked for duplicates by identifyDuplicates. Results are written to the file "dups.Rda".

Usage

identifyDuplicates(fileName,startRun=1,endRun, shift=5000,intervalSize=10000)

Arguments

fileName
file name prefix without type of the result of hapFabia; Attention no type!
startRun
first interval.
endRun
last interval.
shift
distance between start of adjacent intervals.
intervalSize
number of SNVs in a interval.

Details

IBD segments that are similar to each other are identified and the result is written to the file "dups.Rda". For analysis across a whole chromosome this information is important in order to avoid multiple counting of features from the same IBD segment. Used subsequently to iterateIntervals which analyzes intervals of a chromosome for IBD segments. The information on duplicates (or similar IBD segments) is important for a subsequent run of analyzeIBDsegments to avoid redundancies.

Results are saved in "dups.Rda" which contains

  1. dups (the index of duplicates),
  2. un (the index of non-duplicates),
  3. countsA1 (the counts and mapping to intervals for non-duplicates), and
  4. countsA2 (the counts and mapping to intervals for all IBD segments).

Implementation in R.

References

S. Hochreiter et al., ‘FABIA: Factor Analysis for Bicluster Acquisition’, Bioinformatics 26(12):1520-1527, 2010.

See Also

IBDsegment-class, IBDsegmentList-class, analyzeIBDsegments, compareIBDsegmentLists, extractIBDsegments, findDenseRegions, hapFabia, hapFabiaVersion, hapRes, chr1ASW1000G, IBDsegmentList2excel, identifyDuplicates, iterateIntervals, makePipelineFile, matrixPlot, mergeIBDsegmentLists, mergedIBDsegmentList, plotIBDsegment, res, setAnnotation, setStatistics, sim, simu, simulateIBDsegmentsFabia, simulateIBDsegments, split_sparse_matrix, toolsFactorizationClass, vcftoFABIA

Examples

Run this code
## Not run: 
# #########################################
# ## Already run in "iterateIntervals.Rd" ##
# #########################################
# 
# #Work in a temporary directory.
# 
# old_dir <- getwd()
# setwd(tempdir())
# 
# 
# # Load data and write to vcf file.
# data(chr1ASW1000G)
# write(chr1ASW1000G,file="chr1ASW1000G.vcf")
# 
# #Create the analysis pipeline for extracting IBD segments
# makePipelineFile(fileName="chr1ASW1000G",shiftSize=500,intervalSize=1000,haplotypes=TRUE)
# 
# source("pipeline.R")
# 
# # Following files are produced:
# list.files(pattern="chr1")
# 
# 
# 
# # Next we load interval 5 and there the first and second IBD segment
# posAll <- 5
# start <- (posAll-1)*shiftSize
# end <- start + intervalSize
# pRange <- paste("_",format(start,scientific=FALSE),"_",format(end,scientific=FALSE),sep="")
# load(file=paste(fileName,pRange,"_resAnno",".Rda",sep=""))
# IBDsegmentList <- resHapFabia$mergedIBDsegmentList
# summary(IBDsegmentList)
# IBDsegment1 <- IBDsegmentList[[1]]
# summary(IBDsegment1)
# IBDsegment2 <- IBDsegmentList[[2]]
# summary(IBDsegment2)
# 
# 
# 
# 
# #Plot the first IBD segment in interval 5
# plot(IBDsegment1,filename=paste(fileName,pRange,"_mat",sep=""))
# 
# 
# #Plot the second IBD segment in interval 5
# plot(IBDsegment2,filename=paste(fileName,pRange,"_mat",sep=""))
# 
# setwd(old_dir)
# 
# ## End(Not run)


## Not run: 
# ###here an example of the the automatically generated pipeline
# ### with: shiftSize=5000,intervalSize=10000,fileName="filename"
# 
# #####define intervals, overlap, filename #######
# shiftSize <- 5000
# intervalSize <- 10000
# fileName="filename" # without type
# haplotypes <- TRUE
# dosage <- FALSE
# 
# #####load library#######
# library(hapFabia)
# 
# #####convert from .vcf to _mat.txt#######
# vcftoFABIA(fileName=fileName)
# 
# #####copy haplotype, genotype, or dosage matrix to matrix#######
# if (haplotypes) {
#     file.copy(paste(fileName,"_matH.txt",sep=""), paste(fileName,"_mat.txt",sep=""))
# } else {
#     if (dosage) {
#         file.copy(paste(fileName,"_matD.txt",sep=""), paste(fileName,"_mat.txt",sep=""))
#     } else {
#         file.copy(paste(fileName,"_matG.txt",sep=""), paste(fileName,"_mat.txt",sep=""))
#     }
# }
# 
# #####split/ generate intervals#######
# split_sparse_matrix(fileName=fileName,intervalSize=intervalSize,
# shiftSize=shiftSize,annotation=TRUE)
# 
# #####compute how many intervals we have#######
# ina <- as.numeric(readLines(paste(fileName,"_mat.txt",sep=""),n=2))
# noSNVs <- ina[2]
# over <- intervalSize%/%shiftSize
# N1 <- noSNVs%/%shiftSize
# endRunA <- (N1-over+2)
# 
# 
# #####analyze each interval#######
# #####may be done by parallel runs#######
# iterateIntervals(startRun=1,endRun=endRunA,shift=shiftSize,
# intervalSize=intervalSize,fileName=fileName,individuals=0,
# upperBP=0.05,p=10,iter=40,alpha=0.03,cyc=50,IBDsegmentLength=50,
# Lt = 0.1,Zt = 0.2,thresCount=1e-5,mintagSNVsFactor=3/4,
# pMAF=0.03,haplotypes=haplotypes,cut=0.8,procMinIndivids=0.1,thresPrune=1e-3,
# simv="minD",minTagSNVs=6,minIndivid=2,avSNVsDist=100,SNVclusterLength=100)
# 
# #####identify duplicates#######
# identifyDuplicates(fileName=fileName,startRun=1,endRun=endRunA,
# shift=shiftSize,intervalSize=intervalSize)
# 
# #####analyze results; parallel#######
# anaRes <- analyzeIBDsegments(fileName=fileName,startRun=1,endRun=endRunA,
# shift=shiftSize,intervalSize=intervalSize)
# print("Number IBD segments:")
# print(anaRes$noIBDsegments)
# print("Statistics on IBD segment length in SNVs (all SNVs in the IBD segment):")
# print(anaRes$avIBDsegmentLengthSNVS)
# print("Statistics on IBD segment length in bp:")
# print(anaRes$avIBDsegmentLengthS)
# print("Statistics on number of individuals belonging to IBD segments:")
# print(anaRes$avnoIndividS)
# print("Statistics on number of tagSNVs of IBD segments:")
# print(anaRes$avnoTagSNVsS)
# print("Statistics on MAF of tagSNVs of IBD segments:")
# print(anaRes$avnoFreqS)
# print("Statistics on MAF within the group of tagSNVs of IBD segments:")
# print(anaRes$avnoGroupFreqS)
# print("Statistics on number of changes between major and minor allele frequency:")
# print(anaRes$avnotagSNVChangeS)
# print("Statistics on number of tagSNVs per individual of an IBD segment:")
# print(anaRes$avnotagSNVsPerIndividualS)
# print("Statistics on number of individuals that have the minor allele of tagSNVs:")
# print(anaRes$avnoindividualPerTagSNVS)
# 
# #####load result for interval 50#######
# posAll <- 50 # (50-1)*5000 = 245000: interval 245000 to 255000
# start <- (posAll-1)*shiftSize
# end <- start + intervalSize
# pRange <- paste("_",format(start,scientific=FALSE),"_",
# format(end,scientific=FALSE),sep="")
# load(file=paste(fileName,pRange,"_resAnno",".Rda",sep=""))
# IBDsegmentList <- resHapFabia$mergedIBDsegmentList # $
# 
# summary(IBDsegmentList)
# #####plot IBD segments in interval 50#######
# plot(IBDsegmentList,filename=paste(fileName,pRange,"_mat",sep=""))
#    ##attention: filename without type ".txt"
# 
# #####plot the first IBD segment in interval 50#######
# 
# IBDsegment <- IBDsegmentList[[1]]
# plot(IBDsegment,filename=paste(fileName,pRange,"_mat",sep=""))
#    ##attention: filename without type ".txt"
# 
# ## End(Not run)


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