Description Usage Arguments Value References Examples
Refine muscle-invasive bladder cancer into four subtypes based on transcriptome profile by nearest template prediction algorithm.
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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. |
A figure of predictive heatmap by NTP (.pdf) and a data.frame storing the results of nearest template prediction.
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).
1 2 3 4 5 6 7 8 9 | 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)
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