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.
QCcode(x)# S4 method for ChipInfo
QCcode(x)
QCcode(x) <- value
# S4 method for ChipInfo
QCcode(x) <- value
QCpass(x)
QCfail(x, type = NA)
# S4 method for ChipInfo
QCpass(x)
# S4 method for ChipInfo
QCfail(x, type = NA)
a ChipInfo object
new pass/fail codes, e.g, 0,1,...,n
integer between 1 and 100, failure type (user can assign own coding scheme)
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