refineMIBC: Refine muscle-invasive bladder cancer

In xlucpu/refineMIBC: Refine muscle-invasive bladder cancer

Description

Refine muscle-invasive bladder cancer into four subtypes based on transcriptome profile by nearest template prediction algorithm.

Usage

refineMIBC(
  expr = NULL,
  scaleFlag = TRUE,
  centerFlag = TRUE,
  distance = "cosine",
  seed = 123456,
  doPlot = FALSE,
  fig.path = getwd(),
  fig.name = "NTP_PREDICTED_HEATMAP",
  res.path = getwd(),
  res.name = "PREDICTED_MIBC_SUBTYPE"
)

Arguments

expr	A numeric expression matrix with row features and sample columns.
scaleFlag	A logic value to indicate if the expression data should be further scaled. TRUE by default.
centerFlag	A logic value to indicate if the expression data should be further centered. TRUE by default.
distance	A string value to indicate the distance measurement. Allowed values contain c('cosine', 'pearson', 'spearman', 'kendall'); 'cosine' by default.
seed	An integer value for p-value reproducibility; 123456 by default.
doPlot	A logic value to indicate whether to produce prediction heatmap; FALSE by default.
fig.path	A string value to indicate the output path for storing the nearest template prediction heatmap.
fig.name	A string value to indicate the name of the nearest template prediction heatmap.
res.path	A string value to indicate the path for saving the prediction result.
res.name	A string value to indicate the name of the output prediction table.

Value

A figure of predictive heatmap by NTP (.pdf) and a data.frame storing the results of nearest template prediction.

References

Hoshida, Y. (2010). Nearest Template Prediction: A Single-Sample-Based Flexible Class Prediction with Confidence Assessment. PLoS ONE 5, e15543.

Eide, P.W., Bruun, J., Lothe, R.A. et al. CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models. Sci Rep 7, 16618 (2017).

Examples

library(refineMIBC)
load(system.file("extdata", "demo.RData", package = "refineMIBC", mustWork = TRUE)) # load example data
expr <- demo$MIBC.expr
subt <- demo$MIBC.subt
iCS  <- refineMIBC(expr       = expr,
                   scaleFlag  = TRUE,
                   centerFlag = TRUE,
                   doPlot     = FALSE)
head(iCS)

xlucpu/refineMIBC documentation built on Jan. 14, 2022, 8:35 p.m.