validateLibraryFrame: Validate Library names/locations in a Dataframe

In BenaroyaResearch/BRIRUtils: R utilities for RNA-seq processing at BRI

Description

validate standard RNA-seq data: counts, design, metrics, and summary files.

Usage

validateLibraryFrame(counts, design, metrics = NULL, summary = NULL,
  countsField = "colnames", designField = "libraryId",
  metricsField = "libraryId", summaryField = "libraryId")

Arguments

counts	counts dataframe
design	design dataframe
metrics	metrics dataframe (optional)
summary	summary dataframe (optional)
countsField	counts library field - usually column names
designField	design library field - either the row names, or a column in the dataframe
metricsField	metrics library field - either the row names, or a column in the dataframe
summaryField	metrics library field - either the row names, or a column in the dataframe

Value

boolean - side effect of stopping if names are not aligned.

Author(s)

Scott R Presnell, [e-mail]

Examples

counts  <- read.csv(file="data/P239-1_CCLKLANXX_180806_combined_counts.csv", row.names=1)
counts  <- counts[,order(colnames(counts))]
design  <- read.csv(file="data/P239-1 Final Adjusted Annotation.csv", stringsAsFactors = F)
libpattern <- "lib[0-9]+"
colnames(counts)  <- str_extract(colnames(counts), libpattern)
validateLibraryFrame(counts, design)

BenaroyaResearch/BRIRUtils documentation built on May 8, 2019, 1:15 p.m.