loadPathoscopeReports {PathoStat} | R Documentation

## Loads all data from a set of PathoID reports. For each column in the PathoID report, construct a matrix where the rows are genomes and the columns are samples. Returns a list where each element is named according to the PathoID column. For example, ret[["Final.Best.Hit.Read.Numbers"]] on the result of this function will get you the final count matrix. Also includes elements "total_reads" and "total_genomes" from the first line of the PathoID report.

### Description

Loads all data from a set of PathoID reports. For each column in the PathoID report, construct a matrix where the rows are genomes and the columns are samples. Returns a list where each element is named according to the PathoID column. For example, ret[["Final.Best.Hit.Read.Numbers"]] on the result of this function will get you the final count matrix. Also includes elements "total_reads" and "total_genomes" from the first line of the PathoID report.

### Usage

    loadPathoscopeReports(reportfiles, nrows = NULL)

### Arguments

`reportfiles` | Paths to report files
`nrows` | Option to read first N rows of PathoScope reports

### Value

Returns a list where each element is named according to the PathoID column. For example, ret[["Final.Best.Hit.Read.Numbers"]] on the result of this function will get you the final count matrix. Also includes elements "total_reads" and "total_genomes" from the first line of the PathoID report.

### Examples

    input_dir <- system.file("example/data", package = "PathoStat")
    reportfiles <- list.files(input_dir, pattern = "*-sam-report.tsv",
    full.names = TRUE)

[Package PathoStat version 1.12.0 Index]