loadPathoscopeReports: Loads all data from a set of PathoID reports. For each column...

In PathoStat: PathoStat Statistical Microbiome Analysis Package

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)

PathoStat documentation built on Nov. 8, 2020, 5:28 p.m.