View source: R/collapseFullCoverage.R
collapseFullCoverage | R Documentation |
For a given data set this function collapses the full coverage information for each sample from all the chromosomes. The resulting information per sample is the number of bases with coverage 0, 1, etc. It is similar to using table() on a regular vector. This information is then used by sampleDepth for calculating the sample depth adjustments. The data set can loaded to R using (see fullCoverage) and optionally filtered using filterData.
collapseFullCoverage(fullCov, colsubset = NULL, save = FALSE, ...)
fullCov |
A list where each element is the result from
loadCoverage used with |
colsubset |
Which columns of |
save |
If |
... |
Arguments passed to other methods and/or advanced arguments. Advanced arguments:
|
A list with one element per sample. Then per sample, a list with two vector
elements: values
and weights
. The first one is the coverage
value and the second one is the number of bases with that value.
Leonardo Collado-Torres
fullCoverage, sampleDepth
## Collapse the coverage information for the filtered data
collapsedFull <- collapseFullCoverage(list(genomeData),
verbose = TRUE
)
collapsedFull
## Not run:
## You can also collapsed the raw data
collapsedFullRaw <- collapseFullCoverage(list(genomeDataRaw), verbose = TRUE)
## End(Not run)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.