GSEPD_PCA_Plot {rgsepd} | R Documentation |
After processing the pipeline, users may want to have further PCA figures generated. This function takes a completed GSEPD object and generates informative figures, based on the differentially expressed genes.
GSEPD_PCA_Plot(GSEPD)
GSEPD |
The master object, it should have already been run through GSEPD_Process(). |
No return value. Generates files.
GSEPD_PCA_Spec
data("IlluminaBodymap") data("IlluminaBodymapMeta") set.seed(1000) #fixed randomness isoform_ids <- Name_to_RefSeq(c("HIF1A","EGFR","MYH7","CD33","BRCA2")) rows_of_interest <- unique( c( isoform_ids , sample(rownames(IlluminaBodymap), size=500,replace=FALSE))) G <- GSEPD_INIT(Output_Folder="OUT", finalCounts=round(IlluminaBodymap[rows_of_interest , ]), sampleMeta=IlluminaBodymapMeta, COLORS=c("green","black","red")) G <- GSEPD_ChangeConditions( G, c("A","B")) #set testing groups first! G <- GSEPD_Process( G ) #have to have processed results to plot them GSEPD_PCA_Plot(G)