process_phenotypes: Process phenotypes for mapping

In AndersenLab/cegwas2: C. elegans genome-wide association

Description

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

Usage

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.