computeSscore: Computes GCS-score values

In harrisgm/GCSscore: GCSscore: an R package for microarray analysis for Affymetrix/Thermo Fisher arrays

Computes GCS-score values

Description

This internally called function computes the GCS-score values between two Affymetrix-style microarrays. The computeSscore function contains the majority of the GCS-score algorithm.

Usage

computeSscore(cel1, cel2, probeFile, bgp, method, infoKey, SF1 = NULL, SF2 = NULL, 
              verbose = FALSE, trim = NULL, clean.chip)

Arguments

cel1	The 1st Affymetrix CEL file, as read in by the affxparser package
cel2	The 2nd Affymetrix CEL file, as read in by the affxparser package
probeFile	The internal datafile that contains the probe groupings and annotations for each array type and method type
bgp	The index of the probe location, GC-content, and annotations of the background probes of a given chip type. For WT-type arrays, the bgp consists of 16,943 antigenomic background probes. For 3' IVT arrays, the MisMatch (MM) probes are used to calculate the bgp list in both methods
method	Determines the method used to group and tally the probes when calculating GCS-score values
infoKey	The key of how to group the probes together for the GCS-score calculations. Determines the method used to group and tally the probes when calculating GCS-score values. For example, exon-level analysis groups probes by probeset_ids while gene-level groups probes by transcript_cluster_ids
SF1	If the user has predetermined scaling factors, input user Scaling Factor (SF) for the 1st CEL file. Otherwise, the computeSscore function will caluclate SF1 directly from the 1st CEL file
SF2	If the user has predetermined scaling factors, input user Scaling Factor (SF) for the 2nd CEL file. Otherwise, the computeSscore function will caluclate SF2 directly from the 2nd CEL file
verbose	If set to TRUE, additional information will be printed to the console while the algorithm is running.
trim	Internal parameter determined by chip type .trim=0.04 for WT-type arrays and 0.02 for 3' IVT type arrays
clean.chip	The clean chiptype name, based on the platform design package name.

Details

This internally called function computes the raw difference scores between the probes on each microarray, then groups the probes into probesets or transcript cluset ids, and normalizes the results to produce GCS-score values. The function returns the values to the main GCscore2, where BioConductor-based annotations are added to either the exon-level or gene-level probe groupings

Value

A data.table object with GCS-Score values for the probe groupings (determined by the method argument)

Examples

if (length(list.files(path = ".", pattern = "*.CEL")) != 0){

#Example of input, as the function would be called internally:
computeSscore(cel1, cel2, probeFile, bgp, infoKey, method, SF1 = NULL, SF2 = NULL,
              verbose = FALSE, trim = NULL)
}

harrisgm/GCSscore documentation built on Jan. 1, 2023, 12:04 a.m.