read_NGS_raw {CNVgears} | R Documentation

## Read raw copyratio/LRR data for NGS intervals

### Description

`read_NGS_raw`

### Usage

    read_NGS_raw(
      DT_path,
      rds_path,
      pref,
      suff,
      chr_col,
      start_col,
      end_col,
      raw_col,
      raw_type,
      sample_list,
      markers
    )

### Arguments

`DT_path,` | path to the input file.
`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`.
`chr_col,` | name of the column containing the chromosome information in the input file.
`start_col,` | name of the column containing the start information in the input file.
`end_col,` | name of the column containing the end information in the input file.
`raw_col,` | name of the column containing the marker-level raw data in the input file.
`raw_type,` | character, it describes the format in which the LRR-like data is give. Can be either "log2R", "numeric_CN" or "copyratio", see description.
`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.

### Details

This function handles the input, pre-processing and temporary storage (as RDS files) of the the markers-level raw data for each sample. Those are mostly required for CNVs inheritance detection. Any marker-level log2R-like measure is supported, given that, for somatic chromosomes: $$LRR = log2R = log2(CopyRatio) = log2(numeric_CN/2*)$$ Input must be one file per sample.

### Value

nothing, this function saves the results on disk.

[Package CNVgears version 1.0.0 Index]