Description Usage Arguments Value
View source: R/gwas_mappings.R
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.
1 2 3 4 | 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)
|
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 |
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. |
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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