ParseMetaFromGtfFile


    Path to the GTF file that will be parsed.


gtfFilePath


    File pattern that indicates where FASTA file(s) for the associated reference genome can be found.


fastaFilePattern


   Path where the output file will be stored.


outFilePath


   One or more feature types (for example, "protein_coding," "unprocessed_pseudogene") that should be extracted from the GTF file. The default is "protein_coding."


featureTypes


  The type of attribute ("gene_id", "transcript_id") to be parsed. Values will be grouped according to these attributes.


attributeType


  When applying the <code><a rd-options="" href="/link/UPC_RNASeq?package=SCAN.UPC&version=2.14.0" data-mini-rdoc="SCAN.UPC::UPC_RNASeq">UPC_RNASeq</a></code> function, it is possible to correct for the length and GC content of genomic features. To accomplish this, an annotation file indicating these values for each feature must be provided. This helper function enables users to generate an annotation file, using a GTF file and genome FASTA file as references.


SCAN is a microarray normalization method to facilitate
personalized-medicine workflows. Rather than processing
microarray samples as groups, which can introduce biases and
present logistical challenges, SCAN normalizes each sample
individually by modeling and removing probe- and array-specific
background noise using only data from within each array. SCAN
can be applied to one-channel (e.g., Affymetrix) or two-channel
(e.g., Agilent) microarrays. The Universal exPression Codes
(UPC) method is an extension of SCAN that estimates whether a
given gene/transcript is active above background levels in a
given sample. The UPC method can be applied to one-channel or
two-channel microarrays as well as to RNA-Seq read counts.
Because UPC values are represented on the same scale and have
an identical interpretation for each platform, they can be used
for cross-platform data integration.

Stephen R Piccolo

SCAN.UPC

Single-channel array normalization (SCAN) and Universal
exPression Codes (UPC)

ParseMetaFromGtfFile function

Path to the GTF file that will be parsed.

File pattern that indicates where FASTA file(s) for the associated reference genome can be found.

Path where the output file will be stored.

One or more feature types (for example, "protein_coding," "unprocessed_pseudogene") that should be extracted from the GTF file. The default is "protein_coding."

The type of attribute ("gene_id", "transcript_id") to be parsed. Values will be grouped according to these attributes.

When applying the <code><a href="UPC_RNASeq" rd-options="">UPC_RNASeq</a></code> function, it is possible to correct for the length and GC content of genomic features. To accomplish this, an annotation file indicating these values for each feature must be provided. This helper function enables users to generate an annotation file, using a GTF file and genome FASTA file as references.

ParseMetaFromGtfFile: Helper function to parse length and GC content information from a GTF file.

Description

Usage

Arguments

Examples