Description Usage Arguments Details Value
View source: R/process_mappings.R
calculate_VE
calculates the variance explained (VE) for significant SNPs by using the
the spearman rank correlation coefficient.
1 | calculate_VE(mapping_df, phenotype_df)
|
mapping_df |
the output from the |
phenotype_df |
two element list. element 1 : traits. element 2: trait values with strains in columns with each row corresponding to trait in element 1 |
This function requires three inputs, two of which are provided by the user and the other is loaded by the package.
Outputs a two element list that contains two dataframes.
The first data frame is a processed mappings dataframe that contains the same columns
as the output of gwas_mappings
with two additional columns. One that contains
the bonferroni corrected p-value (BF) and another that contains an identifier 1,0 if
the indicated SNP has a higher -log10 value than the bonferroni cut off or not, respectively
The second data frame contains the variance explained data as well as all of the information from the first element.
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