Description Usage Arguments Value Examples
View source: R/expressionModel.R
Run BADGER expression-only model to assess posterior probability of CNVs given normalized expression data only
1 | calcGexpCnvProb(gexp, fits, m, region, gos, quiet = TRUE)
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gexp |
Normalized gene expression matrix |
fits |
Fit for variance around mean |
m |
Expected mean deviation due to copy number change |
region |
Region of interest such as expected CNV boundaries |
gos |
Gene position table |
quiet |
Boolean for whether to suppress progress display |
List of posterior probabilities for amplification and deletion
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | data('MM16.counts')
mat <- log2(MM16.counts + 1)
data('Normal.counts')
mat.ref <- log2(Normal.counts + 1)
mats <- normalizedExpression(mat, mat.ref)
gexp <- mats[[1]]
fits <- mvFit(gexp)
region <- data.frame('chr'=1, start=0, end=1e9)
set.seed(0)
library(biomaRt) ## for gene coordinates
mart.obj <- useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = 'hsapiens_gene_ensembl', host = "jul2015.archive.ensembl.org")
gos <- getBM(values=rownames(gexp),attributes=c("ensembl_gene_id","chromosome_name","start_position","end_position"),filters=c("ensembl_gene_id"),mart=mart.obj)
gos$pos <- (gos$start_position + gos$end_position)/2
results <- calcGexpCnvProb(gexp, fits, 0.15, region, gos)
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