GCSscore {GCSscore} | R Documentation |
The main function used to call and run the GCS-score algorithm.
GCSscore(celFile1 = NULL, celFile2 = NULL, celTable = NULL,celTab.names = FALSE, typeFilter = 1, method = 1, rm.outmask = FALSE, SF1 = NULL, SF2 = NULL, fileout = FALSE, gzip = FALSE, verbose = FALSE)
celFile1 |
If a one comparison run is desired, enter the filename and path to the 1st Affymetrix CEL file |
celFile2 |
If a one comparison run is desired, enter the filename and path to the 2nd Affymetrix CEL file |
celTable |
If a batch run is desired, enter the filename and path to the CSV file containing the batch information |
celTab.names |
If set to |
typeFilter |
If set to |
method |
This determines the method used to group and tally the probes_ids when calculating GCS-scores. For Whole Transcriptome (WT) arrays, for gene-level (transcript_cluster_id-based) analysis, set |
rm.outmask |
If set to |
SF1 |
Input a pre-determined Scaling Factor (SF) for the 1st CEL file |
SF2 |
Input a pre-determined Scaling Factor (SF) for the 2nd CEL file |
fileout |
Determines if the resulting GCS-score output is written to disk in a CSV format following the completion of the function. By default, this is set to FALSE so unnecessary GCS-score outputs are not saved to disk after each run |
gzip |
If set to |
verbose |
If set to |
The input accepts individual CEL files or reads in a CSV file for batch runs. The user also inputs parameters to determine the method
used by the GCS-score algorithm to group and tally the individual probes on a given array.
An ExpressionSet
object with GCS-score values for the probe groupings (determined by the method
argument) and the relevant annotation informtaion
if (length(list.files(path = ".", pattern = "*.CEL")) != 0){ ##Single run example: # get the path to example CEL files in the package directory: celpath1 <- system.file("extdata/ex_dat", "MN_2_3.CEL", package = "GCSscore") celpath2 <- system.file("extdata/ex_dat", "MN_4_1.CEL", package = "GCSscore") # run GCSscore() function directly on two .CEL files: Ss2_clarS <- GCSscore(celFile1 = celpath1, celFile2 = celpath2) # display selected columns of GCSscore output: Ss2_clarS[1:6,c(1,3,6,7,8,11)] ## Batch run example: # get the path to example CSV file in the package directory: celtab_path <- system.file("extdata/ex_dat", "Ss2_BATCH_example.csv", package = "GCSscore") # read in the .CSV file with fread(): celtab <- fread(celtab_path) # view structure of 'celTable' input: celtab # For the following example, the .CEL files are not in the working # directory. The path to the .CEL files must be added to allow # the GCSscore() function to find them. # add path to celFile names in batch input: path <- system.file("extdata/ex_dat", "", package = "GCSscore") celtab$CelFile1 <- celtab[,paste(path,CelFile1,sep="")] celtab$CelFile2 <- celtab[,paste(path,CelFile2,sep="")] # run GCSscore() function with batch input: Ss_clarS_batch <- GCSscore(celTable = celtab, celTab.names = TRUE) # display selected columns of GCSscore batch output: Ss_clarS_batch[1:6,c(1,3,11,12,13,14,15,16)] }