write_variant_influences: Write significant cape interactions to a csv file

In TheJacksonLaboratory/CAPE: Combined Analysis of Pleiotropy and Epistasis for Diversity Outbred Mice

Write significant cape interactions to a csv file

Description

This function takes in the final data object and writes the variant influences that are at or below the specified significance level.

Usage

write_variant_influences(
  data_obj,
  p_or_q = 0.05,
  include_main_effects = TRUE,
  filename = "Variant.Influences.csv",
  delim = ",",
  mark_covar = FALSE,
  write_file = TRUE
)

Arguments

data_obj	a Cape object
p_or_q	A threshold indicating the maximum adjusted p value considered significant. If an FDR method has been used to correct for multiple testing, this value specifies the maximum q value considered significant.
include_main_effects	Whether to include main effects (TRUE) or only interaction effects (FALSE) in the output table.
filename	A character vector specifying the name of the file.
delim	A character string indicating the delimiter in the data file. The default indicates a comma-separated file (",").
mark_covar	A logical value. If TRUE, an asterisk is appended the names of markers used as covariates in the pair scan.
write_file	A logical value indicating whether the table should be written to a file or simply returned.

Details

The columns of the output file are the following: Source: The marker that is the source of the directed interaction Chr: The chromosome on which the source marker lives Position: The genomic position of the source marker Target: If the effect is an interaction, this column lists the marker that is the target of the directed interaction. If the effect is a main effect, this column lists the trait that is the target of the main effect. Chr: The chromosome on which the target marker lives. If the effect is a main effect, this is listed as 0. Position: The genomic position of the target marker. If the effect is a main effect, this is listed as 1. Conditioning: If the effect is a main effect, this column identifies the marker on which the main effect marker was conditioned when it had it's largest main effect. Chr: If the effect is a main effect, this column lists the chromosome on which the conditioning marker lives Position: If the effect is a main effect, this column lists the genomic position of the conditioning marker. Effect: The effect size of the effect, either main effect or interaction. SE: The standard error of the effect, either main effect or interaction. |Effect|/SE: The standardized effect P_empirical: The empirical p value calculated from permutations p_adjusted: The p value adjusted by the method specified in the parameter file.

Value

If write_file is TRUE, this function writes the results table to a file and invisibly returns the table. If write_file is FALSE, the function returns the results table without writing to file.

Examples

## Not run: 
inf_table <- write_variant_influences(data_obj)

## End(Not run)

TheJacksonLaboratory/CAPE documentation built on Feb. 12, 2024, 4:32 p.m.