Description Usage Arguments Details Value Author(s)
This function retrieves bin count for all samples in the input file information data.frame. It was designed to count reads in a small amount of bins (a subset of what will be used for the full analysis). This counts can be used later to compare a potentially large number samples and guide the selection of samples to consider in the analysis.
1 2 | quick.count(files.df, bins.df, nb.cores = 1, col.files = NULL,
nb.rand.bins = NULL, ...)
|
files.df |
a data.frame with the information about the files to use. Columns 'sample' and 'bam' are required. |
bins.df |
a data.frame with the information about the bins. Columns 'chr', 'start' and 'end' are required. |
nb.cores |
number of cores to use. If higher than 1, |
col.files |
if non-NULL, the name of the column in 'files.df' with the filenames where the information should be retrieved from. |
nb.rand.bins |
if non-NULL, the number of bins to randomly choose. Default is NULL. |
... |
extra paramaters for 'bin.bam' function |
If ‘col.files="bc.gc.gz"', for example, the bin counts will be merged from the pre-computed files (the ones created by functions ’bin.bam' and 'correct.GC').
a data.frame with the bin location and read counts for all samples.
Jean Monlong
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