Description Usage Arguments Details Value
View source: R/min_filter_counts.R
This function filters a counts object, removing genes that do not meet a minimum count value in a minimum percentage of libraries
1 | min_filter_counts(counts, min_count=NULL, min_cpm=NULL, min_libs_perc=0.15)
|
counts |
a matrix or data frame of gene expression counts; should have samples in columns and genes in rows. |
min_count |
numeric value, the minimum count value. Either this or min_cpm should be specified, but not both. |
min_cpm |
numeric values, the minimum counts per million value. Either this or min_cpm should be specified, but not both. |
min_libs_perc |
numeric value, the minimum percentage of libraries with counts or cpm equal to or greater than the threshold. |
Genes are removed from counts
if they do not have at least min_count
counts in at least min_libs_perc
Note that adding or removing libraries to/from the counts object may change the genes that meet these thresholds.
a filtered matrix or data frame with the same number of columns as counts
, and potentially fewer rows. Counts are retained in the units they are input (using min_cpm does not convert counts to cpm).
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