cegwas_map: cegwas_map

In AndersenLab/cegwas: A set of functions to process phenotype data, perform GWAS, and perform post-mapping data processing for C. elegans.

Description

cegwas_map is a convenience function takes trait data for a set of strains and performs a mapping - returning a processed mapping data frame. map wraps process_pheno, gwas_mappings, and process_mappings into a single function.

Usage

cegwas_map(trait_data, cores = parallel::detectCores(),
  remove_strains = TRUE, kin_matrix = kinship, snpset = snps,
  duplicate_method = "first", BF = NA, mapping_snp_set = TRUE,
  snp_grouping = 200)

Arguments

cores	number of cores on computer that you want to allocate for mapping. Default value is 4
remove_strains	Remove strains with no known isotype. Default is FALSE.
kin_matrix	is a strainXstrain matrix. default kinship matrix is described above.
duplicate_method	Method for dealing with the presence of multiple strains falling into the same isotype. Either "average" to average phenotypes or "first" to take the first observation.
BF	defines a custom bonferroni correction.
mapping_snp_set	Use simulation based snps when TRUE. Use 5% cut when FALSE.
snp_grouping	defines grouping of peaks. Defined further below, default is 200.
data	two element list. element 1 : traits. element 2: trait values with strains in columns with each row corresponding to trait in element 1
snps	is a set of mapping snps.

Value

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.

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