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Get Start and End chromosomal positions from physical positions

I have a dataset, specifically this data set: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi GSE 76730 sample data set with only one column listing the 'physical positions' Wilting data set used as sample in running CGHCall for CNV in R, with both start and end positions given

I need to run copy number variation analysis on this data using CGHCall package in R. But it seems that in order to run the analysis, I must have both, the start and the end positions, and not simply one column that lists the physical position. What could be a possible way to obtain start and end positions from the physical position given in the GSE 76730 data set? Alternatively, if there's a way to use CGHCall in order to get results without having both the start and end position listed, that would be welcome too.

Thank you for your time.

snp cghcall
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written by ss0083 • ss0083

That R package looks quite new, so, it may not be that well supported. Why not just use the aroma.affymetrix package? The Aroma project has been in existence for many years and are still updating their packages, which are mainly aimed at copy number dtetermination on Affymetrix microarrays.

For the chip used by GSE76730 (the original dataset was actually GSE28582), see: Vignette: Total copy number analysis using CRMA v1 (10K, 100K, 500K)

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written by Kevin Blighe Kevin Blighe

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