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Read and process input data file

ReadFile.Rd

Read and process input data file

Usage

ReadFile(filePath)

Arguments

filePath

Input file path

Value

Processed data.frame

Details

Any lines starting with '#' are ignored to avoid reading template formatting. Pivots the data from wide form into a tidy/long format. Splits the Sample column by "_" into SampleID, Group and Batch columns. Then splits the Group column Subgroup1 and Subgroup2 on "-". The "-" in the Group column is replaced with "_" to prevent issues with making contrasts that need a "-" to delineate between contrast groups. The Metabolite column is split on "_" to identify the extraction method. All values <= 0 are set to NA and other values log2 transformed. The following requirements must be met for this function to work correctly:

  • Sample column data in the form "SampleID_Subgroup1-Subgroup2_Batch"

  • Metabolite column data in the form "MetaboliteName_ExtractionMethod" All numeric batch numbers have padding zeroes stripped and the Batch column is converted to a factor.