process_phenotypes: Process phenotypes for mapping

Description Usage Arguments Value

Description

process_phenotypes takes input raw phenotype data and converts strain names to isotype names, summarizes replicate data, and eliminates outliers.

Usage

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process_phenotypes(df, summarize_replicates = "mean",
  prune_method = "BAMF", remove_outliers = TRUE, threshold = 2)

Arguments

df

a dataframe with a strain column and columns for each trait for processing.

summarize_replicates

summarization method, currently limited to "mean" or "median"

prune_method

method for eliminating outliers, currently limited to "BAMF", "Z", "TUKEY", "MAD"

remove_outliers

boolean to specify if outliers should be eliminated within the function. If FALSE, additional columns will be output specifying if the strain phenotype is an outier.

threshold

integer value defining the threshold for outlier removal, default = 2

Value

Output is a dataframe with


AndersenLab/cegwas2 documentation built on Aug. 26, 2020, 4:43 p.m.