Mixing
R: Passing a single list of matrices as input to a function that requires at least 2 input matrices
1
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?
r list matrix
asked Nov 22 '18 at 8:12
user31888user31888
1007
add a comment |
1
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?
r list matrix
asked Nov 22 '18 at 8:12
user31888user31888
1007
add a comment |
1
1
1
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?
r list matrix
asked Nov 22 '18 at 8:12
user31888user31888
1007
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?
r list matrix
r list matrix
asked Nov 22 '18 at 8:12
user31888user31888
1007
asked Nov 22 '18 at 8:12
user31888user31888
1007
edited Nov 22 '18 at 8:15
user31888
asked Nov 22 '18 at 8:12
user31888user31888
1007
asked Nov 22 '18 at 8:12
user31888user31888
1007
asked Nov 22 '18 at 8:12
user31888user31888
1007
1007
add a comment |
add a comment |
1 Answer
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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 .
answered Nov 22 '18 at 8:30
Thriving For PerfectionThriving For Perfection
517
Works great, thanks !
– user31888
Nov 22 '18 at 8:34
add a comment |
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1 Answer
1
active
oldest
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1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
1
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 .
answered Nov 22 '18 at 8:30
Thriving For PerfectionThriving For Perfection
517
Works great, thanks !
– user31888
Nov 22 '18 at 8:34
add a comment |
1
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 .
answered Nov 22 '18 at 8:30
Thriving For PerfectionThriving For Perfection
517
Works great, thanks !
– user31888
Nov 22 '18 at 8:34
add a comment |
1
1
1
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 .
answered Nov 22 '18 at 8:30
Thriving For PerfectionThriving For Perfection
517
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 .
answered Nov 22 '18 at 8:30
Thriving For PerfectionThriving For Perfection
517
answered Nov 22 '18 at 8:30
Thriving For PerfectionThriving For Perfection
517
answered Nov 22 '18 at 8:30
Thriving For PerfectionThriving For Perfection
517
answered Nov 22 '18 at 8:30
Thriving For PerfectionThriving For Perfection
517
517
Works great, thanks !
– user31888
Nov 22 '18 at 8:34
add a comment |
Works great, thanks !
– user31888
Nov 22 '18 at 8:34
Works great, thanks !
– user31888
Nov 22 '18 at 8:34
Works great, thanks !
– user31888
Nov 22 '18 at 8:34
add a comment |
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