QC-methods: Access quality control pass or fail codes for ChipInfo

In humarray: Simplify Analysis and Annotation of Human Microarray Datasets

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)

## S4 method for signature 'ChipInfo'
QCcode(x)

QCcode(x) <- value

## S4 replacement method for signature 'ChipInfo'
QCcode(x) <- value

QCpass(x)

QCfail(x, type = NA)

## S4 method for signature 'ChipInfo'
QCpass(x)

## S4 method for signature 'ChipInfo'
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 codes

QCcode<-: updates the object specified with new pass/fail codes for the 'QCcode' slot

QCpass: ChipInfo object for which SNPs pass quality control

QCfail: ChipInfo object for which SNPs fail quality control

humarray documentation built on Nov. 20, 2017, 1:05 a.m.