hapFabia (version 1.14.0)

IBDsegmentList2excel: Store an IBD segment list in EXCEL / csv format

Description

IBDsegmentList2excel: R implementation of IBDsegmentList2excel.

IBD segment list is stored in a file in EXCEL format, more precise in comma separated format (.csv).

Usage

"IBDsegmentList2excel"(IBDsegmentList,filename)

Arguments

IBDsegmentList

list of IBD segments given as an object of the class IBDsegmentList.

filename

name of the file where the IBD segment list is stored in EXCEL format.

Value

writes to comma separated .csv file

Details

IBD segment list is stored in comma separate format (.csv) which can readily be read by EXCEL.

The EXCEL (.csv) file contains following columns:

1. ID: number of the IBD segment in the current extraction.
2. bicluster_id: ID of the bicluster the IBD segment was found in.
3. chromosome: the chromosome.
4. IBDsegmentPos: genomic location of the IBD segment.
5. IBDsegmentLength: length of the IBD segment.
6. numberIndividuals: number of samples belonging to the IBD segment.
7. numbertagSNVs: number tagSNVs marking the IBD segment.
8. individuals: IDs of individuals or chromosomes belonging to the IBD segment.
9. tagSNVs: IDs of SNVs that mark the IBD segment (tagSNVs).
10. populationIndividuals: the population each individual belongs to.
11. idIndividuals: IDs of the individuals or chromosomes.
12. labelIndividuals: label of the individuals.
13. platformIndividuals: for each individual the technology/platform that was used to genotype it.
14. coreClusterIndividuals: IDs of individuals that constitute the core of the IBD segment.
15. tagSNVPositions: physical positions of the tagSNVs on the chromosome in base pairs.
16. tagSNVAlleles: alleles of the tagSNVs in the form Ref:Alt where Ref denotes reference allele and Alt the alternative allele.
17. tagSNVNames: name of the tagSNVs according to a given annotation.
18. tagSNVFreq: frequency of tagSNVs in the whole data set.
19. tagSNVGroupFreq: frequency of tagSNVs in the population that is considered.
20. 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.
21. tagSNVsPerIndividual: for each sample: tagSNVs are counted for which the sample has the minor allele.
22. individualPerTagSNV: for each tagSNV: samples are counted for which the SNV has its minor allele.
23. 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.

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

old_dir <- getwd()
setwd(tempdir())

data(hapRes)
mergedIBDsegmentList <- hapRes$mergedIBDsegmentList
IBDsegmentList2excel(IBDsegmentList=mergedIBDsegmentList,
   filename="testResult.csv")

setwd(old_dir)