Description Usage Arguments Value See Also Examples
bayes.risk
function performs by runing Bayesian risk inference model when priors are set by user and liklihood is calculated from given data of SNVs/InDels.
1 2 3 4 |
sample.mutations |
data frame with SNVs and InDels in MAF like format.
Columns (with exactly same names) which
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bcgr.prob |
a numeric vector, same lenght as genes (should be same orderd also) which gives probability of gene having somatic mutation in healfy population.
There are functions for obtaining this vector: |
genes |
vector of genes which were sequenced. They should be unique values of Hugo_Symbol column (with possibility of more additional genes which did not have any SNV/Indel. in given cohort). Default NULL. |
prior.sick |
a numeric value representing incidence of tumor in population. Set by default to 0.0045 . |
Variant_Classification |
(optional) integer/numeric value indicating column in |
Hugo_Symbol |
(optional) integer/numeric value indicating column in |
Tumor_Sample_Barcode |
(optional) integer/numeric value indicating column in |
CCF |
(optional) integer/numeric value indicating column in |
Damage_score |
(optional) integer/numeric value indicating column in |
mode |
a charechter value indicationg how to solve when in one gene-sample pair there are multiple mutations. Options are SUM, MAX and ADVANCE |
epsilon |
a numeric value. If mode is ADVANCE, epsilone value will be threshold for CCF difference to decide if they are in same or different clone. |
a data frame with ranked genes by posteriory probability of gene beeing risk factor for developing tumor. Additional columns with usefull info are contained in data frame.
bcgr
, bcgr.lawrence
and bcgr.combine
for obtaining bcgr.prob variable.
1 2 3 4 5 6 7 | # first calculate CCF
sample.genes.mutect <- CCF(sample.genes.mutect)
# then somatic background probability
bcgr.prob <- bcgr.combine(sample.genes.mutect)
# bayes risk model
risk.genes <- bayes.risk(sample.genes.mutect, bcgr.prob, prior.sick = 0.00007)
head(risk.genes)
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