dumpQCfiles: dump QC (NAs, flags, XY stats) and (optionally) SNP calls and...

In ttriche/sesamizeGEO: the poor man's methylation suite (cf. `sesamizer`)

dump QC (NAs, flags, XY stats) and (optionally) SNP calls and beta values

Description

NA fraction, median CN, control flags, XY stats are saved in stub_QC.csv.gz SNP calls are saved in stub_SNPcalls.csv.gz if snps == TRUE SNP intensities are saved in stub_SNPs.csv.gz if snps == TRUE Sesamized betas are saved in stub_betas.csv.gz if betas == TRUE

Usage

dumpQCfiles(grSet, stub = NULL, path = ".", snps = TRUE, betas = FALSE)

Arguments

grSet	GenomicRatioSet with betas and QC metrics to dump out
stub	mandatory prefix for derived files (e.g. stub_QC.csv.gz)
path	where to save the dumped CSV files (".")
snps	dump SNPs and SNP calls? (TRUE)
betas	dump beta values too? (FALSE)

Value

       the status of the final operation

See Also

      SNPcalls

ttriche/sesamizeGEO documentation built on Nov. 12, 2023, 5:42 p.m.