read_finalreport_snps {CNVgears} | R Documentation

## Read Illumina array raw data

### Description

`read_finalreport` handles inputs of data in FinalReport-like format

### Usage

    read_finalreport_snps(
      DT_path,
      mark_ID_col = "SNP Name",
      chr_col = "Chr",
      pos_col = "Position"
    )

### Arguments

`DT_path,` | path to the input file.
`mark_ID_col,` | name of the column containing the SNP ID information in the input file. Default is `"SNP Name"`.
`chr_col,` | name of the column containing the chromosome information in the input file. Default is `"Chr"`.
`pos_col,` | name of the column containing the SNPs position information in the input file. Default is `"Position"`.

### Details

This function is used to load data in FinalReport like format into a `data.table` containing the SNPs markers information (i.e. chromosome and position). The function expect a single file where each markers is present one single time. Similar files are often required or produced by the calling algorithm/pipeline, e.g. the PFB file in PennCNV can be used here.

### Value

a `data.table`, will be of `Markers` class in future versions.

### Examples

    DT <- read_finalreport_snps(system.file("extdata", "SNP.pfb", package = "CNVgears"),
    mark_ID_col = "Name", chr_col = "Chr", pos_col = "Position")

[Package CNVgears version 1.0.0 Index]