IBDsegmentList2excel {hapFabia} | R Documentation

## 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

    ## S4 method for signature 'IBDsegmentList,character'
    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.

### 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.

### Value

writes to comma separated `.csv` file

### 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

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

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

    setwd(old_dir)

[Package hapFabia version 1.22.0 Index]