Description Usage Arguments Details Value References Examples
bcgr.lawrence
function calculates the background probability that a gene is mutated based on the background somatic mutation rate
provided in the Lawrence paper.
1 2 3 |
sample.mutations |
data frame in MAF like format.
Columns names/header in
|
genes |
vector of genes which were sequenced.
Vector of unique values of Hugo_Symbol names (with possibility of more additional genes which did not have any SNV in the cohort).
Default is NULL value and then the list of the unique genes is taken from |
lengthGenes |
numeric vector of the lengths (suquenced) for all |
Variant_Classification |
(optional) integer/numeric value indicating which column in |
Hugo_Symbol |
(optional) integer/numeric value indicating which column in |
Tumor_Sample_Barcode |
(optional) integer/numeric value indicating which column in |
CCF |
(optional) integer/numeric value indicating which column in |
Function uses sample.mutations
to estimate the expected number of nonsilent mutations per patient.
a numeric vector of the probabilites that a gene has a nonsilent mutation (not caused by cancer).
http://www.ncbi.nlm.nih.gov/pubmed/23770567.
1 2 | bcgr.L <- bcgr.lawrence(sample.genes.mutect, length.genes$Hugo_Symbol, length.genes$Coverd_len)
head(bcgr.L)
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