makeCalls.PC1ihc {PCAPAM50}

Make intermediate intrinsic subtype calls

Description

This function processes clinical IHC subtyping data and preprocessed PAM50 gene expression data to form a gene expression-guided ER-balanced set.This set is created by combining IHC classification information and using principal component 1 (PC1) to guide the separation.The function computes the median for each gene in this ER-balanced set, updates a calibration file, and runs subtype prediction algorithms to generate intermediate intrinsic subtype calls based on the PAM50 method. Various diagnostics and subtyping results are returned.

Usage

makeCalls.PC1ihc(df.cln, seed = 118, mat, inputDir=NULL)

Arguments

df.cln

Data frame of clinical data; It should include the columns 'PatientID' and 'IHC'.

seed

Seed for random number generation to ensure reproducibility. Default is 118.

mat

Matrix of preprocessed PAM50 expression data.

inputDir

Directory for output files.If NULL, a subdirectory named "Calls.PC1ihc" 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.

PC1cutoff

Cutoff values for PC1 used in subsetting.

DF.PC1

Data frame of initial PCA results merged with clinical data.

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)


  

  # Call the function
  result <- makeCalls.PC1ihc(df.cln=df.cln, seed = 118, mat = Test.matrix, inputDir=NULL)