Description Usage Arguments Value
View source: R/data_preparation.R
This function removes sites in SNP, sex-chromosomal, or non-CG context.
1 2 |
rnb.set |
An object of type |
snp |
Flag indicating if snps are to be removed. Either SNPs annotated in the RnBeads annotation object of specified as an
additional file with one SNP identifier per row in |
snp.list |
Path to a file containing known SNPs. One SNP identifier should be present per row. |
somatic |
Flag indicating if only somatic probes are to be kept. |
context |
Flag indicating if probes in non-CpG context are to be removed. |
qual.filter |
Vector of indices removed during quality filtering. |
dist.snps |
Flag indicating of potential SNPs are to be determined by selecting those sites that have trimodally distributed (differences 0, 0.5 and 1.0) pairwise differences across the samples. |
A vector of indices of sites surviving the annotation filter criteria.
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