Description Usage Arguments Details Value Author(s) References Examples
The method normalizes count data by rarefying
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e_data |
a p \times n data.frame of count data, where p is the number of features and n is the number of samples. Each row corresponds to data for a feature, with the first column giving the feature name. |
edata_id |
character string indicating the name of the feature identifier. Usually obtained by calling |
size |
the library size to rarefy down to. Default uses the minimum sample size. |
Count data is normalized by rarefying, subsampling samples down to a specified library size. If the specified library size is larger than a sample's library size, the sample will be discarded. A warning message will display which samples are discarded. This normalization method is likely not the best course of action.
List containing 4 elements: norm_data is a data.frame with same structure as e_data that contains the rarefied data, location_param is NULL, and scale_param is the library size counts were rarefied to.
Allison Thompson
McMurdie, Paul J., and Susan Holmes. "Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible." PLOS Computational Biology. 10.4 (2014)
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