allele-methods: Access alleles for ChipInfo

In humarray: Simplify Analysis and Annotation of Human Microarray Datasets

Description

A1/A2: Returns the letter for the A1/A2 alleles for the chip object, e.g, 'A','C','G','T', etc Only if these are annotated internally, or else a vector of NAs

A1<-/A2<-: Allows user to set the allele codes for each SNP of the chip object, e.g, A,C,G,T,K, etc. If you are using allele codes this is likely to necessary as each genotyping produces a different set of allele codes. If using in conjunction with snpStats, remember that allele codes are always flipped to be alphabetical, so the reference allele is the later letter in the alphabet. Note, assignment to A2 needs to be done separately.

Usage

A1(x)

## S4 method for signature 'ChipInfo'
A1(x)

A2(x)

## S4 method for signature 'ChipInfo'
A2(x)

A1(x) <- value

## S4 replacement method for signature 'ChipInfo'
A1(x) <- value

A2(x) <- value

## S4 replacement method for signature 'ChipInfo'
A2(x) <- value

Arguments

x	a ChipInfo object
value	new allele codes, e.g, A,C,G,T

Value

character vector of allele codes (or NAs)

A1<-: updates the ChipInfo object specified with new allele codes for the 'A1' slot

A2<-: updates the ChipInfo object specified with new allele codes for the 'A2' slot

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