Description Usage Arguments Value Examples
CCF
function calculates CCF for each variant based on its
allele frequency, CNV/ploidy context, cancer cell fraction of reporeted CNVS within variant position and purity of tumor tissue.
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sample.mutations |
Data Frame which should follow MAF format. Columns (with exactly same names) which
If not provided they need to be specifed as paramiters of the CCF function. |
VAF |
(optional) integer/numeric value indicating column in |
ploidy |
(optional) integer/numeric value indicating column in |
CCF_CNV |
(optional) integer/numeric value indicating column in |
purity |
(optional) integer/numeric value indicating column in |
correct |
(optional, default = TRUE) Correction to perform on SNVs for which CCF is calculated as larger then 1. This is justifed with rough estimation of VAF values, missing CNVs and violation of mutal exclusivit assumption (two mutatations in same gene/patient are in different cancer frations ). It is recomanted to keep this parameter to TRUE value, othervise unrealistic CCF (> 1) values can be returned for some SNVs. |
a data frame with one additional column, giving CCF vlaues for each SNV in intial sample.mutations
data frame.
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