seqSummary: Summarize a SeqArray GDS File

In SeqArray: Data management of large-scale whole-genome sequence variant calls

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/Summary.R

Description

Gets the summary of SeqArray GDS file.

Usage

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seqSummary(gdsfile, varname=NULL, check=c("default", "none", "full"), verbose=TRUE) 

Arguments

Details

If check="default", the function performs regular checking, like variable dimensions. If check="full", it performs more checking, e.g., unique sample id, unique variant id, whether genotypic data are in a valid range or not.

Value

If varname=NULL, the function returns a list:

— seqSummary(gdsfile, "genotype", check="none", verbose=FALSE) returns a list with components:

— seqSummary(gdsfile, "allele") returns a data.frame with ID and descriptions (check="none"), or a list with components:

— seqSummary(gdsfile, "$alt") returns a data.frame with ID and Description for describing the alternative alleles.

— seqSummary(gdsfile, "annotation/filter") or seqSummary(gdsfile, "$filter") returns a data.frame with ID and description (check="none"), or a list with components: value (a data.frame with ID and Description), table (cross tabulation for the variable 'filter').

— seqSummary(gdsfile, "annotation/info") or seqSummary(gdsfile, "$info") returns a data.frame describing the variables in the folder "annotation/info" with ID, Number, Type, Description, Source and Version.

— seqSummary(gdsfile, "annotation/format") returns a data.frame describing the variables in the folder "annotation/format" with ID, Number, Type and Description.

— seqSummary(gdsfile, "sample.annotation") returns a data.frame describing sample annotation with ID, Type and Description.

— seqSummary(gdsfile, "$reference") returns the genome reference if it is defined (a 0-length character vector if undefined).

— seqSummary(gdsfile, "$contig") returns the contig information, a data.frame including ID.

— seqSummary(gdsfile, "$format") returns a data.frame describing VCF FORMAT header with ID, Number, Type and Description. The first row is used for genotypes.

— seqSummary(gdsfile, "$digest") returns a data.frame with the full names of GDS variables, digest codes and validation (FALSE/TRUE).

Author(s)

Xiuwen Zheng

See Also

seqGetData, seqApply

Examples

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# the GDS file (gds.fn <- seqExampleFileName("gds")) seqSummary(gds.fn) ans <- seqSummary(gds.fn, check="full") ans seqSummary(gds.fn, "genotype") seqSummary(gds.fn, "allele") seqSummary(gds.fn, "annotation/filter") seqSummary(gds.fn, "annotation/info") seqSummary(gds.fn, "annotation/format") seqSummary(gds.fn, "sample.annotation") seqSummary(gds.fn, "$reference") seqSummary(gds.fn, "$contig") seqSummary(gds.fn, "$filter") seqSummary(gds.fn, "$alt") seqSummary(gds.fn, "$info") seqSummary(gds.fn, "$format") seqSummary(gds.fn, "$digest") # open a GDS file f <- seqOpen(gds.fn) # get 'sample.id samp.id <- seqGetData(f, "sample.id") # get 'variant.id' variant.id <- seqGetData(f, "variant.id") # set sample and variant filters seqSetFilter(f, sample.id=samp.id[c(2,4,6,8,10)]) set.seed(100) seqSetFilter(f, variant.id=sample(variant.id, 10)) seqSummary(f, "genotype") # close a GDS file seqClose(f)