calc_mean_cov: Collapse bigwig files into a mean coverage
In dzhang32/ODER: Optimising the Definition of Expressed Regions
Description
Usage
Arguments
Value
Description
calc_mean_cov takes as input a set of bws. Then uses the total AUC to
normalise coverage per sample and finally collapses the coverage for each
sample into a mean coverage.
Usage
1
calc_mean_cov(bw_paths, aucs, target_auc, chr_to_filter)
Arguments
bw_paths
paths to bigwig files.
aucs
vector containing aucs matching the order of bigwig paths.
target_auc
total auc to normalise all samples to. E.g. 40e6 * 100
would be the estimated total auc for sample sequenced to 40 million reads
of 100bp in length.
chr_to_filter
chrs to obtain mean coverage for.
Value
list of Rle objects. Each containing the mean coverage for an entire
chromosome.
dzhang32/ODER documentation built on April 23, 2021, 11:21 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Value
Description
calc_mean_cov takes as input a set of bws. Then uses the total AUC to
normalise coverage per sample and finally collapses the coverage for each
sample into a mean coverage.
Usage
1 | calc_mean_cov(bw_paths, aucs, target_auc, chr_to_filter)
|
Arguments
bw_paths |
paths to bigwig files. |
aucs |
vector containing aucs matching the order of bigwig paths. |
target_auc |
total auc to normalise all samples to. E.g. 40e6 * 100 would be the estimated total auc for sample sequenced to 40 million reads of 100bp in length. |
chr_to_filter |
chrs to obtain mean coverage for. |
Value
list of Rle objects. Each containing the mean coverage for an entire chromosome.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.