Description Usage Arguments Details Value Author(s) References See Also Examples
IBDsegmentList2excel
: R implementation of IBDsegmentList2excel
.
IBD segment list is stored in a file in EXCEL format, more precise in comma separated format (.csv).
1 2 | ## S4 method for signature 'IBDsegmentList,character'
IBDsegmentList2excel(IBDsegmentList,filename)
|
IBDsegmentList |
list of IBD segments given as an object
of the class |
filename |
name of the file where the IBD segment list is stored in EXCEL format. |
IBD segment list is stored
in comma separate format (.csv
) which can readily be read by EXCEL.
The EXCEL (.csv
) file contains following columns:
ID
: number of the IBD segment in the current extraction.
bicluster_id
: ID of the bicluster the IBD segment was found in.
chromosome
: the chromosome.
IBDsegmentPos
: genomic location of the IBD segment.
IBDsegmentLength
: length of the IBD segment.
numberIndividuals
: number of samples belonging to the IBD segment.
numbertagSNVs
: number tagSNVs marking the IBD segment.
individuals
: IDs of individuals or chromosomes belonging to the IBD segment.
tagSNVs
: IDs of SNVs that mark the IBD segment (tagSNVs).
populationIndividuals
: the population each individual belongs to.
idIndividuals
: IDs of the individuals or chromosomes.
labelIndividuals
: label of the individuals.
platformIndividuals
: for each individual the technology/platform that was used to genotype it.
coreClusterIndividuals
: IDs of individuals that constitute the core
of the IBD segment.
tagSNVPositions
: physical positions of the tagSNVs on the
chromosome in base pairs.
tagSNVAlleles
: alleles of the tagSNVs in the form Ref:Alt
where Ref denotes reference allele and Alt the alternative allele.
tagSNVNames
: name of the tagSNVs according to a given annotation.
tagSNVFreq
: frequency of tagSNVs in the whole data set.
tagSNVGroupFreq
: frequency of tagSNVs in the population that is considered.
tagSNVChange
: if the minor allele was more frequent than the
major, then both were switched. Switching is marked by a 1 and
otherwise it is 0.
tagSNVsPerIndividual
: for each sample: tagSNVs are counted for which the sample has the minor allele.
individualPerTagSNV
: for each tagSNV: samples are counted for which the SNV has its minor allele.
tagSNVAnno
: the functional annotation of tagSNVs for each tagSNV: like stop-loss,
stop-gain, non-synonymous, synonymous, promoter, exonic, intronic, intergenic, etc.
Implementation in R.
writes to comma separated .csv
file
Sepp Hochreiter
S. Hochreiter et al., ‘FABIA: Factor Analysis for Bicluster Acquisition’, Bioinformatics 26(12):1520-1527, 2010.
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
1 2 3 4 5 6 7 8 9 10 11 | old_dir <- getwd()
setwd(tempdir())
data(hapRes)
mergedIBDsegmentList <- hapRes$mergedIBDsegmentList
IBDsegmentList2excel(IBDsegmentList=mergedIBDsegmentList,
filename="testResult.csv")
setwd(old_dir)
|
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