process_pheno: Process Phenotype Data

Description Usage Arguments Details Value

View source: R/process_phenotypes.R

Description

process_pheno Processes raw data file for GWAS mapping using gwas_mappings function

Usage

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process_pheno(data, remove_strains = TRUE, duplicate_method = "first",
  use_bamf = TRUE)

Arguments

data

is a dataframe containing phenotype data. The dataframe can be structured in wide or long format.

long format - The first columns should be strain whereas additional columns are traits. One row list a strain followed by all of that strains phenotypes.

strain, trait1, trait2, ...

wide format - The first column should be named trait and subsequent all additional columns should be strains. One row corresponding to one trait for all strains.

trait, strain1, strain2, ...

remove_strains

Remove strains with no known isotype. Default is TRUE.

duplicate_method

Method for dealing with the presence of multiple strains falling into the same isotype. Either "average" or "first".

use_bamf

use bamf prune to remove outliers

Details

This function takes raw phenotype data and eliminates outlier strains with a modified version of bamf_prune from the easysorter package. Additionally it eliminates any traits that have the same values for >95 If multiple strains are present that fall into the same isotype, they can be removed by setting remove_strains to

Value

Outputs a list. The first element of the list is an ordered vector of traits. The second element of the list is a dataframe containing one column for each strain, with values corresponding to traits in element 1 for rows.


AndersenLab/cegwas documentation built on March 6, 2020, 1:10 a.m.