read_finalreport_raw {CNVgears} | R Documentation

## Read Illumina array raw data

### Description

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

### Usage

    read_finalreport_raw(
      DT_path,
      rds_path,
      pref,
      suff,
      sample_list,
      markers,
      chr_col = "Chr",
      pos_col = "Position",
      LRR_col = "Log R Ratio",
      BAF_col = "B Allele Freq"
    )

### Arguments

`DT_path,` | character, the path to the directory with the raw data (i.e. the splitted final reports)
`rds_path,` | path to the directory where RDS should be stored.
`pref, suff,` | eventual prefix an suffix (e.g. ".txt"). If not necessary must be set to `NA`.
`sample_list,` | a `data.table`, the output of `read_metadt`.
`markers,` | a `data.table`, the output of `read_NGS_intervals` or `read_finalreport_snps`, depending on the initial data type.
`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"`.
`LRR_col,` | name of the column containing the LRR information in the input file. Default is `"Log R Ratio"`.
`BAF_col,` | name of the column containing the BAF information in the input file. Default is `"B Allele Freq"`.

### Details

This function handles the input, pre-processing and temporary storage (as RDS files) of the the markers-level raw data for each sample starting from FinalReport-like files (any plain text file with columns header can be read). Input must be one file per sample.

### Value

nothing, this function saves the results on disk.

### Examples

    read_finalreport_raw(DT_path = system.file("extdata", package = "CNVgears"),
                        pref = "Final_report_example", suff = ".txt",
                        rds_path = file.path("tmp_RDS"),
                        markers = markers_examples,
                        sample_list = cohort_examples[sample_ID == "NA12878", ])

[Package CNVgears version 1.0.0 Index]