Description Usage Arguments Value Author(s)
TMM normalization of bin counts. After such normalization, the majority of bins have the same trimmed average across samples.
1 2 |
bc.df |
a data.frame with 'chr', 'start', 'end' columns and then one column per sample with its bin counts. |
cont.sample |
the sample to use as baseline for the pairwise normalization. All the samples will be normalized to it. |
trim.level |
How much of the M values should be trimmed (on each side of the distribution). Default is 0.3 (30%). |
nb.cores |
the number of cores to use. Default is 1. |
norm.stats.comp |
Should some statistics on the normalized bin count be computed (mean, sd, outliers). Default is TRUE. |
a list with
norm.stats |
a data.frame witht some metrics about the normalization of each bin (row) : coverage average and standard deviation; number of outlier samples |
bc.norm |
a data.frame, similar to the input 'bc.df', with the normalized bin counts. |
Jean Monlong
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