buildCodesetAnnotation: Build NanoString codeset annotation

In NanoStringQCPro: Quality metrics and data processing methods for NanoString mRNA gene expression data

Description

This function returns a data frame whose content is the combination of the NanoString-provided codeset annotation (.RLF file and the "Design Data" tab of the CDR spreadsheet) with gene annotation in the org.Hs.eg.db package.

Usage

buildCodesetAnnotation(rlf = NULL, cdrDesignData = NULL,
  removeRedundantCols = TRUE, addEgAnnotations = FALSE)

Arguments

rlf	Path to the RLF file
cdrDesignData	Path to a manually prepared .CSV export of the "Design Data" tab of the CDR file (optional; see 'details' section below for how the export should be prepared)
removeRedundantCols	Logical. If TRUE, cols in the CDR that are redundant with those in the RLF will be omitted from the output.
addEgAnnotations	Logical indicating whether or not to add EntrezGene IDs and HGNC symbols from the org.Hs.eg.db package.

Details

The original NanoString provided .RLF file is expected as input. This file is the master (i.e. only probes listed here will be annotated; any extra ones in the CDR export will be dropped). If the CDR "Design Data" .CSV is specified, the function expects this .CSV file to be generated from the "Design Data" tab of the original NanoString provided Excel CDR file. This tab needs to be trimmed by skipping the NanoString header and first column containing only integers; the resulting .CSV should contain the actual table (including its header – beginning with "Customer Identifier"). The function will match and join the .RLF and CDR .CSV using their "ProbeID" and "NSID" fields, and then it will add gene annotation (EntrezGene ID, HGNC symbol, and chromosomal position) by doing lookups in the org.Hs.eg.db package using the RefSeq accessions from the RLF.

Value

A data frame whose content is the combination of the NanoString-provided codeset annotation with gene annotation in the org.Hs.eg.db package.

Author(s)

Dorothee Nickles, Robert Ziman

Examples

rlf <- system.file("extdata", "RLF", "NQCP_example.rlf", package="NanoStringQCPro")
cdrDesignData <- system.file("extdata", "CDR", "CDR-DesignData.csv", package="NanoStringQCPro")
annot <- buildCodesetAnnotation(rlf, cdrDesignData)

NanoStringQCPro documentation built on Nov. 8, 2020, 8:11 p.m.