Learn R Programming
humarray (version 1.0.0)

QCcode: Access quality control pass or fail codes for ChipInfo

Description

Returns the pass or fail codes for each SNP of the chip object, e.g, 0,1,..,n etc Only if these are added manually, or else all will be 'pass' (=0)

QCcode<-: Allows user to set the pass or fail codes for each SNP of the chip object, e.g, 0,1,..,n etc. 0 is always pass, >0 is always fail, but each integer can be used to represent a different failure type, or for simplicity, stick to 0 and 1, ie, just pass and fail.

QCpass: Returns the subset of the ChipInfo object for which SNPs pass quality control, according to the QCcodes() slot == 0.

QCfail: Returns the subset of the ChipInfo object for which SNPs fail quality control, according to the QCcodes() slot > 0.

Usage

QCcode(x)


"QCcode"(x)


QCcode(x) <- value


"QCcode"(x) <- value


QCpass(x)


QCfail(x, type = NA)


"QCpass"(x)


"QCfail"(x, type = NA)

Arguments

x
a ChipInfo object
value
new pass/fail codes, e.g, 0,1,...,n
type
integer between 1 and 100, failure type (user can assign own coding scheme)

Value

integer vector of pass/fail codesQCcode<-: updates the object specified with new pass/fail codes for the 'QCcode' slotQCpass: ChipInfo object for which SNPs pass quality controlQCfail: ChipInfo object for which SNPs fail quality control