meredith: MEREDITH (multi omic data integration approach)

In Kyoko-wtnb/meRedith: MEREDITH (Multi-omic data integration approach)

Description

MEREDITH combines a list of input data (data.frame or matrix) and perform tSNE

Usage

meredith(data, scale = FALSE, transfer = FALSE, takepc = 50,
  explainedVar = FALSE, nTSNE = 100, dims = 2, initial_dims = 50,
  perplexity = 30, theta = 0.5, max_iter = 1000)

Arguments

data	List of matrix or data frame. (Note that even when input is one matrix/dataframe, use list())
transfer	Logical. TRUE if the input matrix/data frame have to be transfered. Default is FALSE.
takepc	Integer. The number of PC to keep. Default is 50.
nTSNE	Integer. The number of run for tSNE. Default is 100.
dims, initial_dims, preplexity, theta, max_iter	option of Rtsne (see ?Rtsne).
Logical.	The scale option for PCA (see ?prcomp). Default is FALSE
explainedvar	FALSE or a value. The percentage of explained variance to keep. Default is FALSE. If this argument is value between 0 and 100, takepc will be ignored.

Value

list of data same as the Rtsne output (see ?Rtsne for details)

Kyoko-wtnb/meRedith documentation built on May 8, 2019, 5:40 p.m.