makeCalls.v1PAM {PCAPAM50}

Make PCAPAM50 calls

Description

This function uses the intermediate intrinsic subtype calls and preprocessed PAM50 gene expression data to create an ER-balanced set and produces PCAPAM50 Calls.

Usage

makeCalls.v1PAM(df.pam, seed = 118, mat, inputDir=NULL)

Arguments

df.pam

Data frame of PAM data; It should include the columns 'PatientID' and 'PAM50'.

seed

Seed for random number generation to ensure reproducibility.

mat

Matrix of preprocessed PAM50 expression data.

inputDir

Directory for output files.If NULL, a subdirectory named "Calls.PCAPAM50" within the temporary directory will be used.

Value

Returns a list containing:

Int.sbs

Data frame with integrated subtype and clinical data.

score.fl

Data frame with scores from subtype predictions.

mdns.fl

Data frame with median values for each gene in the ER-balanced set.

SBS.colr

Colors associated with each subtype from the prediction results.

outList

Detailed results from subtype prediction functions.

See Also

prcomp, merge, set.seed

Examples

  data_path <- system.file("extdata", "Sample_IHC_PAM_Mat.Rdat", package = "PCAPAM50")
  load(data_path) # Loads Test.ihc and Test.matrix


  # Prepare the data
  Test.ihc$ER_status <- rep("NA", length(Test.ihc$PatientID))
  Test.ihc$ER_status[grep("^L",Test.ihc$IHC)] = "pos"
  Test.ihc$ER_status[-grep("^L",Test.ihc$IHC)] = "neg"
  Test.ihc <- Test.ihc[order(Test.ihc$ER_status, decreasing = TRUE),]
  Test.matrix <- Test.matrix[, Test.ihc$PatientID]

  df.cln <- data.frame(PatientID = Test.ihc$PatientID, IHC = Test.ihc$IHC, stringsAsFactors = FALSE)
  inputDir <- "Call.PC1"

  # Make a secondary ER-balanced subset and derive intermediate intrinsic subtype calls
  result <- makeCalls.PC1ihc(df.cln=df.cln, seed = 118, mat = Test.matrix, inputDir=inputDir)

  df.pc1pam = data.frame(PatientID=result$Int.sbs$PatientID,
  			PAM50=result$Int.sbs$Int.SBS.Mdns.PC1ihc,
			IHC=result$Int.sbs$IHC,
			stringsAsFactors=FALSE) ### IHC column is optional
  
  

  # Make a tertiary ER-balanced set and PCAPAM50 calls
  res <- makeCalls.v1PAM(df.pam = df.pc1pam, seed = 118, mat = Test.matrix, inputDir=NULL)