Loop over DNA intervals with a call of hapFabia

Description

iterateIntervals: R implementation of iterateIntervals.

Loops over all intervals and calls hapFabia and then stores the results. Intervals have been generated by split_sparse_matrix.

Usage

iterateIntervals(startRun=1,endRun,shift=5000,intervalSize=10000,
   annotationFile=NULL,fileName,prefixPath="",
   sparseMatrixPostfix="_mat",annotPostfix="_annot.txt",
   individualsPostfix="_individuals.txt",individuals=0,
   lowerBP=0,upperBP=0.05,p=10,iter=40,quant=0.01,eps=1e-5,
   alpha=0.03,cyc=50,non_negative=1,write_file=0,norm=0,
   lap=100.0,IBDsegmentLength=50,Lt = 0.1,Zt = 0.2,
   thresCount=1e-5,mintagSNVsFactor=3/4,pMAF=0.03,
   haplotypes=FALSE,cut=0.8,procMinIndivids=0.1,thresPrune=1e-3,
   simv="minD",minTagSNVs=6,minIndivid=2,avSNVsDist=100,SNVclusterLength=100)

Arguments

Details

Implementation in R. Reads annotation of the individuals if available, then calls hapFabia and stores its results. Results are saved in EXCEL format and as R binaries.

iterateIntervals loops over all intervals and calls hapFabia and then stores the results. Intervals have been generated by split_sparse_matrix. The results are the indentified IBD segments which are stored separately per interval. A subsequent analysis first calls identifyDuplicates to identify IBD segments that are found more than one time and then analyzes the IBD segments by analyzeIBDsegments.

The SNV annotation file ..._annot.txt contains:

1. first line: number individuals;

2. second line: number SNVs;

3. for each SNV a line containing following field that are blank separated: "chromosome", "physical position", "snvNames", "snvMajor", "snvMinor", "quality", "pass", "info of vcf file", "fields in vcf file", "frequency", "0/1: 1 is changed if major allele is actually minor allele".

The individuals annotation file, which name is give to annotationFile, contains per individual a tab separated line with

1. id;

2. subPopulation;

3. population;

4. platform.

Value

Loop over DNA intervals with a call of hapFabia

Author(s)

Sepp Hochreiter

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

## 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=0.035,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)

#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 haplotype data (1000Genomes)
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)