describeStore: collect basic descriptive statistics on ciseStore instances

In gQTLBase: gQTLBase: infrastructure for eQTL, mQTL and similar studies

Description

collect basic descriptive statistics on ciseStore instances

Usage

describeStore(st, genetag = "probeid", snptag = "snp", ids = NULL,
                 resfilter = force, doChecks = TRUE, ...)
describeByFilts(st, filtlist, ...)

Arguments

st	instance of ciseStore-class
genetag	string for field name for name of quantitatively assayed feature, defaults to "probeid"; for GTEx application "gene" is used
snptag	string for field name for name of genotype feature
ids	integerish vector of ids, can be left NULL to survey entire store
resfilter	function applied to job results prior to summarization, defaults to force()
filtlist	a list of functions suitable as resfilter arguments
doChecks	logical – if true, will collect information on match between number probes requested and number reported on, and two scans of VCF loci in cis to probes. See details.
...	used with describeByFilts, pass to storeApply

Details

uses parallel infrastructure of foreach on contents managed by st@reg

describeByFilts returns a matrix of descriptions with one row per filtlist element

storeDescription holds results of a describe task and includes information on noncongruence of features with cis tests and of results of two distinct scans of VCF: one with readGT on a single sample, the other with readVcf on all samples. If there are discrepancies between features given and tests returned, [storeDescription]@reqfail will give the job ids for these. If there are discrepancies between the numbers of loci retrieved on the two VCF scans, @locfail will tive the job ids for these. @reqfail events may be legitimate when a feature has no SNP in cis at the given radius. @locfail events usually indicate an I/O problem and the jobs should be resubmitted.

Value

list with elements ntests, ngene.uniq, nsnp.uniq

Examples

## Not run: 
 library(geuvStore2)
 mm = makeGeuvStore2()
 describeStore(mm, ids=1:10, resfilter=function(x) x[x$mindist < 50000])
 
## End(Not run)

gQTLBase documentation built on Nov. 8, 2020, 7:07 p.m.