cape (version 2.0.2)

writeVariantInfluences: Write the final results to a file

Description

This function takes in the final data object and writes the variant influences that are at or below the specified significance level to a file in the current working directory.

Usage

writeVariantInfluences(data.obj, p.or.q = 0.05, 
filename = "Variant.Influences.csv", delim = ",", 
mark.covar = FALSE, write.file = TRUE)

Arguments

data.obj

The object in which all results are stored. See read.population.

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. Only marker pairs with p or q values below this threshold will be plotted.

filename

A character vector specifying the name of the file.

delim

A character string indicating the delimeter 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.

Value

This function writes a table of direct influences to a file. It also returns the table invisibly, i.e. if the output of the function is assigned to an object, the object will contain the table of influences. Otherwise, nothing is returned.

Examples

# here the table is written to a file, but nothing is returned.
## Not run: writeVariantInfluences(obesity.cross)

# here the table is written to a file, and returned to the 
# object sig.table
## Not run: 
# 	sig.table <- writeVariantInfluences(obesity.cross)
# 	print(sig.table)## End(Not run)