Skip to contents

Load all data files for EWAS module

Upload sample data and methylation data for EWAS analysis. Users can either read external .csv/.xlsx files with ExpoPath and MethyPath, or pass data objects already loaded in the R environment with ExpoData and MethyData.

Usage

loadEWAS(input, ExpoPath = NULL, MethyPath = NULL, ExpoData = "default",
MethyData = "default")

Arguments

  • input:

    An R6 class integrated with all the information obtained from the initEWAS function.

  • ExpoPath:

    The path to store the user's sample data. Each row represents a sample, and each column represents a variable (exposure variable or covariate). Both .csv and .xlsx file types are supported. The first column must be the sample ID, which must be consistent with the IDs in the methylation data.

  • MethyPath:

    The path to store the user's methylation data. Each row represents a CpG site, and each column represents a sample. Both .csv and .xlsx file types are supported. The first column must be the CpG probes. The sample IDs must be consistent with the IDs in the sample data.

  • ExpoData:

    The data.frame of the user-supplied sample data that has been loaded into the R environment. If default, the example data inside the package is used. The first column must be the sample name.

  • MethyData:

    The data.frame of the user-supplied methylation data that has been loaded into the R environment. If default, an example of methylation data inside the package is loaded. The first column must be the CpG site name.

Value

input, an R6 class object integrating all information.

Examples

if (FALSE) { # \dontrun{
res <- initEWAS(export = FALSE)
res <- loadEWAS(input = res, ExpoData = "default", MethyData = "default")
} # }