GSEPD_ChangeConditions: GSEPD_ChangeConditions

In rgsepd: Gene Set Enrichment / Projection Displays

Description

This function is an interface to set which samples are the test conditions. Don't forget to GSEPD_Process() after changing settings. If you want to systematically try each condition pairing, try GSEPD_ProcessAll()

Usage

GSEPD_ChangeConditions(GSEPD, newConditions)

Arguments

GSEPD	Parameters object.
newConditions	a two-item vector matching some of your sampleMeta$Conditions

Details

Interface will check if the conditions are known, then set the C2T value.

Value

Returns the GSEPD parameter object with its mode set via the C2T and Conditions element of the named list. These tell later steps which sample conditions you intend on comparing.

See Also

GSEPD_Example

Examples

  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=2000,replace=FALSE)))
  G <- GSEPD_INIT(Output_Folder="OUT",
                finalCounts=round(IlluminaBodymap[rows_of_interest , ]),
                sampleMeta=IlluminaBodymapMeta,
                COLORS=c("green","black","red"))
        ConditionsToTest <- c("A","B")
  G <- GSEPD_ChangeConditions( G, ConditionsToTest  )
  #G <- GSEPD_Process( G ) #would test samples A vs samples B
  G <- GSEPD_ChangeConditions( G, c("A","C"))
  #G <- GSEPD_Process( G ) #would test samples A vs samples C

rgsepd documentation built on Nov. 8, 2020, 4:58 p.m.