runNTP: Run nearest template prediction

In xlucpu/MOVICS: Multi-Omics integration and VIsualization in Cancer Subtyping

Description

Using Nearest Template Prediction (NTP) based on predefined templates derived from current identified subtypes to assign potential subtype label on external cohort.

Usage

runNTP(
  expr = NULL,
  templates = NULL,
  scaleFlag = TRUE,
  centerFlag = TRUE,
  nPerm = 1000,
  distance = "cosine",
  seed = 123456,
  verbose = TRUE,
  doPlot = FALSE,
  fig.path = getwd(),
  fig.name = "ntpheatmap",
  width = 5,
  height = 5
)

Arguments

expr	A numeric matrix with row features and sample columns; data is recommended to be z-scored.
templates	A data frame with at least two columns; class (coerced to factor) and probe (coerced to character).
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.
nPerm	An integer value to indicate the permutations for p-value estimation.
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.
verbose	A logic value to indicate whether console messages are to be displayed; TRUE 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.
width	A numeric value to indicate the width of output figure.
height	A numeric value to indicate the height of output figure.

Value

A figure of predictive heatmap by NTP (.pdf) and a list with the following components:

ntp.res a data.frame storing the results of nearest template prediction (see ntp).

clust.res similar to 'clust.res' returned by 'getMOIC()' or 'get

mo.method a string value indicating the method used for prediction.

References

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

Examples

# There is no example and please refer to vignette.

xlucpu/MOVICS documentation built on July 24, 2021, 9:23 p.m.