Description Usage Arguments Details Value See Also Examples
Computes the log-posterior probability distribution for the specified range of cellularity and ploidy parameters
1 2 3 4 5 6 |
cellularity |
vector of cellularity values to be tested. |
ploidy |
vector of ploidy values to be tested. |
mc.cores |
number of cores to use, defined as in
|
... |
any argument accepted by |
baf.model.fit
uses the function baf.bayes
to infer
the log-posterior probability of the model fit using the possible
combinations of cellularity and ploidy values provided in the arguments.
Similarly mufreq.model.fit
fits the mutation/depth ratio model using
the function mufreq.bayes
.
baf.model.fit
is the defalt method used to infer cellularity and
ploidy on segmented chromosomes. The mufreq.model.fit
function
estimates cellularity and ploidy using mutation frequency and depth ratio,
however, the mutation data is more affected to background noise
compared to the segmented B-allele frequency, hence it may give less
accurate results.
A list of three items:
ploidy |
tested values of the ploidy parameter |
cellularity |
tested values of the cellularity parameter |
lpp |
log-posterior probability of each pair of cellularity/ploidy parameters. |
cp.plot
for visualization of the resulting object,
and get.ci
to extract confidence intervals.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 | ## Not run:
data.file <- system.file("extdata", "example.seqz.txt.gz",
package = "sequenza")
# read all the chromosomes:
seqz.data <- read.seqz(data.file)
# Gather genome wide GC-stats from raw file:
gc.stats <- gc.sample.stats(data.file)
gc.normal.vect <- mean_gc(gc.stats$normal)
gc.tumor.vect <- mean_gc(gc.stats$tumor)
# Read only one chromosome:
seqz.data <- read.seqz(data.file, chr_name = "1")
# Correct the coverage of the loaded chromosome:
seqz.data$adjusted.ratio <- round((seqz.data$depth.tumor /
gc.tumor.vect[as.character(seqz.data$GC.percent)]) /
(seqz.data$depth.normal /
gc.normal.vect[as.character(seqz.data$GC.percent)]), 3)
# Select the heterozygous positions
seqz.hom <- seqz.data$zygosity.normal == 'hom'
seqz.het <- seqz.data[!seqz.hom, ]
# Detect breakpoints
breaks <- find.breaks(seqz.het, gamma = 80, kmin = 10,
baf.thres = c(0, 0.5))
# use heterozygous and homozygous position to measure segment values
seg.s1 <- segment.breaks(seqz.data, breaks = breaks)
# filter out small ambiguous segments, and conveniently weight
# the segments by size:
seg.filtered <- seg.s1[(seg.s1$end.pos - seg.s1$start.pos) > 3e6, ]
weights.seg <- (seg.filtered$end.pos - seg.filtered$start.pos) / 1e6
# Set the average depth ratio to 1:
avg.depth.ratio <- 1
# run the BAF model fit
CP <- baf.model.fit(Bf = seg.filtered$Bf,
depth.ratio = seg.filtered$depth.ratio, weight.ratio = weights.seg,
weight.Bf = weights.seg, sd.ratio = seg.filtered$sd.ratio,
sd.Bf = seg.filtered$sd.BAF, avg.depth.ratio = avg.depth.ratio,
cellularity = seq(0.1, 1, 0.01), ploidy = seq(0.5, 3, 0.05))
confint <- get.ci(CP)
ploidy <- confint$max.ploidy
cellularity <- confint$max.cellularity
## End(Not run)
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