GSEPD_ProcessAll: GSEPD_ProcessAll

In kstammits/rgsepd: Gene Set Enrichment / Projection Displays

GSEPD_ProcessAll

Description

Runs each pairing within GSEPD$sampleMeta$Conditions.

Usage

GSEPD_ProcessAll(G)

Arguments

G	The GSEPD object from GSEPD_INIT()

Details

Set your GSEPD$LIMIT before running each pairwise comparison.

Value

Returns the last GSEPD object.

See Also

GSEPD_Process

Examples

  data("IlluminaBodymap")
  data("IlluminaBodymapMeta")
  head(IlluminaBodymap)
  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=2000,replace=FALSE)))
  G <- GSEPD_INIT(Output_Folder="OUT",
                finalCounts=round(IlluminaBodymap[rows_of_interest , ]),
                sampleMeta=IlluminaBodymapMeta,
                COLORS=c("green","black","red"))    
                
#  G <- GSEPD_ProcessAll( G ) #would run across all pairs of G$Condition

kstammits/rgsepd documentation built on Oct. 13, 2022, 6:43 p.m.