Qfyilyi

I am trying to use the R mnnCorrect function (from the scran package). It requires at least 2 input matrices to work.

# install package

source("https://bioconductor.org/biocLite.R"); biocLite("scran")

# example matrix 1

B1 <- matrix(rnorm(10000), ncol=50)

# example matrix 2

B2 <- matrix(rnorm(10000), ncol=50)

# function below works fine

out <- mnnCorrect(B1, B2)

However, I am trying to supply these matrices as a list like so (more convenient for automating the process with a variable number of matrices):

mat_list=list()

mat_list[["Mat1"]]=B1

mat_list[["Mat2"]]=B2

str(mat_list)

List of 2

 $ Mat1: num [1:200, 1:50] 1.107 -0.828 1.559 -1.353 0.667 ...

 $ Mat2: num [1:200, 1:50] -0.231 0.894 0.369 1.606 -1.346 ...



# This works fine

out <- mnnCorrect(mat_list$Mat1, mat_list$Mat2)



# These do not work

out <- mnnCorrect(mat_list)

Error in mnnCorrect(mat_list) : at least two batches must be specified



out <- mnnCorrect(cat(paste(gsub("^","mat_list$",names(mat_list)),collapse=", "))

Error in mnnCorrect(mat_list) : at least two batches must be specified



out <- mnnCorrect(capture.output(cat(paste(gsub("^","mat_list$",names(mat_list)),collapse=", ")))

Error in mnnCorrect(mat_list) : at least two batches must be specified



library(dplyr)

cat(paste(gsub("^","mat_list$",names(mat_list)),collapse=", ") %>% mnnCorrect(.)

mat_list$Mat1, mat_list$Mat2Error in mnnCorrect(.) : at least two batches must be specified

Is there a way to achieve this?

In R, you use the function do.call for that. Here is an example:

do.call(mnnCorrect, mat_list)

See also the help page ?do.call .