Description Usage Arguments Value
This function creates a reference set from a binned counts file
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binned.counts.file |
file name of the binned counts. The binned counts file should be comma delimited, and the first line need to be the chromosome names of each bin |
outcomes |
data.frame with column names: Dx, Gender, SampleID |
combined.counts.fname |
file name to write to for the combined counts per chromosomes, default is not to write result to file |
method |
either "zscore", "NCV" or "MAD", default is zscore |
gcCorrect |
whether to do gc correction or not (True = do the correction) |
gcContentFile |
file name of a Rdata object with the gcContent data |
filterBin |
whether to filter bins based on unusually high counts and high variance, default is to filter |
removeOutlierSamples |
whether to remove samples which has a low correlation value to the rest of the reference set, default is FALSE |
PCA |
whether to do PCA correction or not (True = do the correction) |
numPC |
number of principal components to discard (default = 10) |
masked.counts.file |
file name of the masked counts file |
cleaned.binned.counts.fname |
file name to write to for the corrected binned counts, default is not to write to file |
class of rapidr.ref which can then be used to test unknown samples
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