filterTarget {appreci8R} | R Documentation

## Excludes all off-target calls from further analysis.

### Description

appreci8R combines and filters the output of different variant calling tools according to the 'appreci8'-algorithm. In the 1st analysis step, all off-target calls are excluded from further analysis. A list of data.frames (one list per sample) with all on-target calls is returned.

### Usage

    filterTarget (output_folder, caller_name, caller_folder, caller_file_names_add,
                  caller_file_type, caller_snv_indel, caller_snv_names_add,
                  caller_indel_names_add, caller_chr = 1, caller_pos = 2,
                  caller_ref = 4, caller_alt = 5, targetRegions)

### Arguments

`output_folder` | The folder to write the output files into. If an empty string is provided, no files are written out.
`caller_name` | Name of the variant calling tool (only necessary if an output folder is provided).
`caller_folder` | Folder containing the variant calling results.
`caller_file_names_add` | Suffix for naming the variant calling files. If an empty string is provided, it is assumed that the files only contain the sample name, e.g. "Sample1.vcf".
`caller_file_type` | File type of the variant calling results (".vcf" or ".txt").
`caller_snv_indel` | SNVs and indels are reported in the same file (`TRUE` or FALSE).
`caller_snv_names_add` | Suffix for naming the variant calling files containing SNVs (only evaluated if `caller_snv_indel==FALSE`).
`caller_indel_names_add` | Suffix for naming the variant calling files containing indels (only evaluated if `caller_snv_indel==FALSE`).
`caller_chr` | Column of the variant calling input containing information on chr (default: 1).
`caller_pos` | Column of the variant calling input containing information on pos (default: 2).
`caller_ref` | Column of the variant calling input containing information on ref (default: 4).
`caller_alt` | Column of the variant calling input containing information on alt (default: 5).
`targetRegions` | Data.frame object containing the target regions to be analyzed (bed-format: 1st column chr, 2nd column 0-based start pos, 3rd column 1-based end pos). Or: GRanges object containing the target regions to be analyzed.

### Details

The function `filterTarget` covers two steps: reading input and target filtration.

First, all files in `caller_folder` of the file type `caller_file_type` with the suffix `caller_file_names_add` are read. Sample names are automatically derived from the file names (e.g. a sample name would be called "Sample1" if a file was called "Sample1.txt" and no suffix was defined; a sample would be called "Sample1.mutations" if a file was called "Sample1.mutations.vcf" and no suffix was defined, but "Sample1" if the suffix ".mutations" was defined).

If SNVs and indels are reported in separated files (in the same folder), `caller_snv_indel==TRUE` and `caller_snv_names_add` and `caller_indel_names_add` are defined, input from two files per sample is read and automatically combined (e.g. a sample would be called "Sample1" if files "Sample1.SNV.vcf" and "Sample1.indel.vcf" are read and `caller_snv_indel==TRUE`, `caller_snv_names_add` was defined as ".SNV" and `caller_indel_names_add` was defined as ".indel").

Subsequently, the read variant calling results are filtered according to the defined target region. All off-target calls are excluded from further analysis.

### Value

A list of data.frames is returned. Every list element contains the information on one sample. Every data.frame contains the columns: the SampleID (taken from the input file names), Chr, Pos, Ref and Alt.

### Author(s)

Sarah Sandmann <sarah.sandmann@uni-muenster.de>

### See Also

`appreci8R`, `appreci8Rshiny`, `normalize`, `annotate`, `combineOutput`, `evaluateCovAndBQ`, `determineCharacteristics`, `finalFiltration`

### Examples

    output_folder<-""
    target<-data.frame(chr = c("2","4","12","17","21","X"),
                       start = c(25469500,106196950,12046280,7579470,36164400,15838363),
                       end = c(25469510,106196960,12046350,7579475,36164410,15838366))
    caller_folder <- system.file("extdata", package = "appreci8R")

    targetFiltered<-filterTarget(output_folder, "GATK", caller_folder,
                                 ".rawMutations", ".vcf", TRUE, "", "",
                                 targetRegions = target)

[Package appreci8R version 1.12.1 Index]