readPathoscopeData {PathoStat} | R Documentation

## Reads the data from PathoScope reports and returns a list of final guess relative abundance and count data

### Description

Reads the data from PathoScope reports and returns a list of final guess relative abundance and count data

### Usage

    readPathoscopeData(input_dir = ".",
      pathoreport_file_suffix = "-sam-report.tsv", use.input.files = FALSE,
      input.files.path.vec = NULL, input.files.name.vec = NULL)

### Arguments

`input_dir` | Directory where the tsv files from PathoScope are located
`pathoreport_file_suffix` | PathoScope report files suffix
`use.input.files` | whether input dir to pathoscope files or directly pathoscope files
`input.files.path.vec` | vector of pathoscope file paths
`input.files.name.vec` | vector of pathoscope file names

### Value

List of final guess relative abundance and count data

### Examples

    example_data_dir <- system.file("example/data", package = "PathoStat")
    pathoreport_file_suffix <- "-sam-report.tsv"
    datlist <- readPathoscopeData(example_data_dir, pathoreport_file_suffix,
    input.files.name.vec = as.character(1:6))

[Package PathoStat version 1.13.1 Index]