importNgsLogs {ngsReports} | R Documentation

## Import Various NGS-related log files

### Description

Imports NGS-related log files such as those generated from stderr.

### Usage

    importNgsLogs(x, type = "auto", which, stripPaths = TRUE)

### Arguments

`x` | `character`. Vector of filenames. All log files must be of the same type. Duplicate file paths will be silently ignored.
`type` | `character`. The type of file being imported. Can be one of `bowtie`, `bowtie2`, `hisat2`, `star`, `flagstat`, `featureCounts`, `duplicationMetrics`, `cutadapt`, `macs2Callpeak`, `adapterRemoval`, `quast` or `busco` Defaults to `type = "auto"` which will automatically detect the file type for all implemented types.
`which` | Which element of the parsed object to return. Ignored in all file types except when `type` is set to duplicationMetrics, cutadapt or adapterRemoval. See details for possible values
`stripPaths` | logical(1). Remove paths from the Filename column

### Details

Imports one or more log files as output by tools such as: `bowtie`, `bowtie2`, `featureCounts`, `Hisat2`, `STAR`, `picard MarkDuplicates`, `cutadapt`, `flagstat`, `macs2Callpeak` `Adapter Removal`, `trimmomatic` `quast` or `busco`. `autoDetect` can be used to detect the log type by parsing the file.

The featureCounts log file corresponds to the `counts.out.summary`, not the main `counts.out` file.

Whilst most log files return a single tibble, some are more complex with multiple modules.

`adapterRemoval` can return one of four modules (which = 1:4),. When calling by name, the possible values are sequences, settings, statistics or distribution. Partial matching is implemented.

`cutadapt` can return one of five modules (which = 1:5). When calling by name the possible modules are summary, adapter1, adapter2, adapter3 or overview. Note that adapter2/3 may be missing from these files depending on the nature of your data. If cutadapt log files are obtained using `report=minimal`, all supplied log files must be of this format and no modules can be returned.

`duplicationMetrics` will return either the metrics of histogram. These can be requested by setting which as 1 or 2, or naming either module.

### Value

A `tibble`. Column names are broadly similar to the text in supplied files, but have been modified for easier handling under R naming conventions.

### Examples

    f <- c("bowtiePE.txt", "bowtieSE.txt")
    bowtieLogs <- system.file("extdata", f, package = "ngsReports")
    df <- importNgsLogs(bowtieLogs, type = "bowtie")

[Package ngsReports version 1.8.1 Index]