Description Usage Arguments Details Value
View source: R/process_phenotypes.R
process_pheno
Processes raw data file for GWAS mapping using gwas_mappings
function
1 2 | process_pheno(data, remove_strains = TRUE, duplicate_method = "first",
use_bamf = TRUE)
|
data |
is a dataframe containing phenotype data. The dataframe can be structured in wide or long format.
|
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 |
use_bamf |
use bamf prune to remove outliers |
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
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.
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