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.
loadPathoscopeReports(reportfiles, nrows = NULL)
reportfiles |
Paths to report files |
nrows |
Option to read first N rows of PathoScope reports |
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.
input_dir <- system.file("example/data", package = "PathoStat") reportfiles <- list.files(input_dir, pattern = "*-sam-report.tsv", full.names = TRUE)