Description Usage Arguments Value Examples
Run BADGER allele-only model to assess posterior probability of CNVs given allele information only
1 2 3 | calcAlleleCnvProb(r, cov.sc, l, cov.bulk, region, gtf, mono = 0.7,
pe = 0.01, filter = TRUE, likelihood = FALSE, n.iter = 1000,
quiet = TRUE, delim = ":")
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r |
Matrix of alt allele count in single cells |
cov.sc |
Matrix of coverage in single cells |
l |
Vector of alt allele count in bulk |
cov.bulk |
Vector of coverage in bulk |
region |
Region of interest such as expected CNV boundaries |
gtf |
GTF file contents for mapping SNPs to genes |
mono |
Rate of mono-allelic expression. Default: 0.7 |
pe |
Effective error rate to capture error from sequencing, etc. Default: 0.01 |
filter |
Boolean for whether to filter out SNP sites with no coverage. Default: TRUE |
likelihood |
Boolean for whether to use likelihood based estimate of posterior. Default: FALSE |
n.iter |
Number of iterations in MCMC. Default: 1000 |
quiet |
Boolean of whether to suppress progress bar. Default: TRUE |
delim |
Delimiter for names of SNPs as Chromosome[delim]Position. Default: ":" ex. chr1:283838897 |
Posterior probability of deletion or LOH
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | ## Single cell data
data(snpsHet_MM16ScSample)
## Bulk exome
data(snpsHet_MM16BulkSample)
## Not run:
gtfFile <- 'data-raw/Homo_sapiens.GRCh37.75.gtf'
gtf <- read.table(gtfFile, header=F, stringsAsFactors=F, sep='\t')
## End(Not run)
region <- data.frame('chr'=2, start=0, end=1e9) # deletion region
## Not run:
results <- calcAlleleCnvProb(r, cov.sc, l, cov.bulk, region, gtf)
## End(Not run)
region <- data.frame('chr'=3, start=0, end=1e9) # neutral region
## Not run:
results <- calcAlleleCnvProb(r, cov.sc, l, cov.bulk, region, gtf)
## End(Not run)
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