combat_to_ref: Normalize a given dataset to a reference dataset, using...

In aeolianine/CRCsubtyping: Subtyping Colorectal Expression Data

Normalize a given dataset to a reference dataset, using M-ComBat. Source: https://github.com/aeolianine/M-ComBat/blob/master/MComBatRScript.R Reference: Stein et al, Removing batch effects from purified plasma cell gene expression microarrays with modified ComBat, BMC Bioinformatics2015 16:63, https://doi.org/10.1186/s12859-015-0478-3

Description

Normalize a given dataset to a reference dataset, using M-ComBat. Source: https://github.com/aeolianine/M-ComBat/blob/master/MComBatRScript.R Reference: Stein et al, Removing batch effects from purified plasma cell gene expression microarrays with modified ComBat, BMC Bioinformatics2015 16:63, https://doi.org/10.1186/s12859-015-0478-3

Usage

combat_to_ref(myDataset, refDataset)

Arguments

myDataset	- the given dataset to be normalized
refDataset	- the reference dataset to "be normalized to"

Value

a matrix corresponding to the normalized "myDataset" together with "refDataset" (pasted together column-wise)

Examples

dat1 = cbind(c(1,2,3,3), c(-5,7,3,8), c(10,-4,5,0))
dat2 = cbind(c(10,2.6,-30,39), c(-15,7.4,-3.2,10), c(5,4,-5,0.5))
rownames(dat1) = c('g1', 'g2', 'g3', 'g4')
rownames(dat2) = c('g1', 'g2', 'g3', 'g4')
print(combat_to_ref(dat1, dat2))

aeolianine/CRCsubtyping documentation built on Jan. 13, 2023, 12:16 p.m.