Description Usage Arguments Details Value Examples
View source: R/computeSscore.r
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.
1 2 | computeSscore(cel1, cel2, probeFile, bgp, method, infoKey, SF1 = NULL, SF2 = NULL,
verbose = FALSE, trim = NULL)
|
cel1 |
The 1st Affymetrix CEL file, as read in by the |
cel2 |
The 2nd Affymetrix CEL file, as read in by the |
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 |
method |
Determines the method used to group and tally the probes when calculating GCS-score values |
infoKey |
The |
SF1 |
If the user has predetermined scaling factors, input user Scaling Factor (SF) for the 1st CEL file. Otherwise, the |
SF2 |
If the user has predetermined scaling factors, input user Scaling Factor (SF) for the 2nd CEL file. Otherwise, the |
verbose |
If set to |
trim |
Internal parameter determined by chip type . |
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
A data.table
object with GCS-Score values for the probe groupings (determined by the method
argument)
1 2 3 4 5 6 | 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)
}
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.