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Read in processed data This function is intended to be called after either process_plink() or process_delim() has been called once.

Source: R/get_data.R
get_data.Rd

Read in processed data This function is intended to be called after either process_plink() or process_delim() has been called once.

Usage

get_data(path, returnX = FALSE, trace = TRUE)

Arguments

path

The file path to the RDS object containing the processed data. Do not add the '.rds' extension to the path.

returnX

Logical: Should the design matrix be returned as a numeric matrix that will be stored in memory. By default, this will be FALSE.

trace

Logical: Should trace messages be shown? Default is TRUE.

Value

A list with these components:

  • std_X, the column-standardized design matrix as either (1) a numeric matrix or (2) a filebacked matrix (FBM). See bigstatsr::FBM() and bigsnpr::bigSnp-class documentation for details.

  • (if PLINK data) fam, a data frame containing the pedigree information (like a .fam file in PLINK)

  • (if PLINK data) map, a data frame containing the feature information (like a .bim file in PLINK)

  • ns: A vector indicating the which columns of X contain nonsingular features (i.e., features with variance != 0.

  • center: A vector of values for centering each column in X

  • scale: A vector of values for scaling each column in X