R: How to index R objects within a for loop (Seurat)












0















I'm trying to use a for loop to simplify the following code:



a1 <- CreateSeuratObject (raw.data = a1.data)

a2 <- CreateSeuratObject (raw.data = a2.data)

a3 <- ...


I've tried the following:



samples <- c("a1", "a2", "a3")

samples.data <- c("a1.data", "a2.data", "a3.data")

for (i in samples) {

  for (j in samples.data) {

    i <- CreateSeuratObject(raw.data = j)    

  }

}


But it returns the following error:



Error in base::colSums(x, na.rm = na.rm, dims = dims, ...) : 

 'x' must be an array of at least two dimensions


The CreateSeuratObject function essentially tries to read the samples.data vector instead of indexing the corresponding item in the vector. How can I fix this?






r







share|improve this question























  • This is a bad idea. 1) You are rewriting i every time through the inner loop on j. 2) You are trying to create n = length(samples) objects in the global environment. Instead you should keep the objects in a list.

    – Rui Barradas
    Nov 15 '18 at 7:04
















0















I'm trying to use a for loop to simplify the following code:



a1 <- CreateSeuratObject (raw.data = a1.data)

a2 <- CreateSeuratObject (raw.data = a2.data)

a3 <- ...


I've tried the following:



samples <- c("a1", "a2", "a3")

samples.data <- c("a1.data", "a2.data", "a3.data")

for (i in samples) {

  for (j in samples.data) {

    i <- CreateSeuratObject(raw.data = j)    

  }

}


But it returns the following error:



Error in base::colSums(x, na.rm = na.rm, dims = dims, ...) : 

 'x' must be an array of at least two dimensions


The CreateSeuratObject function essentially tries to read the samples.data vector instead of indexing the corresponding item in the vector. How can I fix this?






r







share|improve this question























  • This is a bad idea. 1) You are rewriting i every time through the inner loop on j. 2) You are trying to create n = length(samples) objects in the global environment. Instead you should keep the objects in a list.

    – Rui Barradas
    Nov 15 '18 at 7:04














0












0








0








I'm trying to use a for loop to simplify the following code:



a1 <- CreateSeuratObject (raw.data = a1.data)

a2 <- CreateSeuratObject (raw.data = a2.data)

a3 <- ...


I've tried the following:



samples <- c("a1", "a2", "a3")

samples.data <- c("a1.data", "a2.data", "a3.data")

for (i in samples) {

  for (j in samples.data) {

    i <- CreateSeuratObject(raw.data = j)    

  }

}


But it returns the following error:



Error in base::colSums(x, na.rm = na.rm, dims = dims, ...) : 

 'x' must be an array of at least two dimensions


The CreateSeuratObject function essentially tries to read the samples.data vector instead of indexing the corresponding item in the vector. How can I fix this?






r







share|improve this question














I'm trying to use a for loop to simplify the following code:



a1 <- CreateSeuratObject (raw.data = a1.data)

a2 <- CreateSeuratObject (raw.data = a2.data)

a3 <- ...


I've tried the following:



samples <- c("a1", "a2", "a3")

samples.data <- c("a1.data", "a2.data", "a3.data")

for (i in samples) {

  for (j in samples.data) {

    i <- CreateSeuratObject(raw.data = j)    

  }

}


But it returns the following error:



Error in base::colSums(x, na.rm = na.rm, dims = dims, ...) : 

 'x' must be an array of at least two dimensions


The CreateSeuratObject function essentially tries to read the samples.data vector instead of indexing the corresponding item in the vector. How can I fix this?






r




r






share|improve this question













share|improve this question











share|improve this question




share|improve this question










asked Nov 15 '18 at 6:36









GLeeGLee

32




32













  • This is a bad idea. 1) You are rewriting i every time through the inner loop on j. 2) You are trying to create n = length(samples) objects in the global environment. Instead you should keep the objects in a list.

    – Rui Barradas
    Nov 15 '18 at 7:04



















  • This is a bad idea. 1) You are rewriting i every time through the inner loop on j. 2) You are trying to create n = length(samples) objects in the global environment. Instead you should keep the objects in a list.

    – Rui Barradas
    Nov 15 '18 at 7:04

















This is a bad idea. 1) You are rewriting i every time through the inner loop on j. 2) You are trying to create n = length(samples) objects in the global environment. Instead you should keep the objects in a list.

– Rui Barradas
Nov 15 '18 at 7:04





This is a bad idea. 1) You are rewriting i every time through the inner loop on j. 2) You are trying to create n = length(samples) objects in the global environment. Instead you should keep the objects in a list.

– Rui Barradas
Nov 15 '18 at 7:04












1 Answer
1






active

oldest

votes


















0














Here are three ways of doing what you want. I suggest you do not use the first way.



samples <- c("a1", "a2", "a3")

samples.data <- c("a1.data", "a2.data", "a3.data")



for (i in seq_along(samples)) {

    assign(samples[i], CreateSeuratObject(raw.data = samples.data[i]))

}



samples_list <- vector("list", length = length(samples))

for (i in seq_along(samples)) {

  samples_list[[i]] <- CreateSeuratObject(raw.data = samples.data[i]))

}

names(samples_list) <- samples



samples_list2 <- lapply(samples.data, CreateSeuratObject)

names(samples_list2) <- samples





share|improve this answer



















  • 1





    Thank you! I ended up going with lapply.

    – GLee
    Nov 15 '18 at 19:25











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1 Answer
1






active

oldest

votes








1 Answer
1






active

oldest

votes









active

oldest

votes






active

oldest

votes









0














Here are three ways of doing what you want. I suggest you do not use the first way.



samples <- c("a1", "a2", "a3")

samples.data <- c("a1.data", "a2.data", "a3.data")



for (i in seq_along(samples)) {

    assign(samples[i], CreateSeuratObject(raw.data = samples.data[i]))

}



samples_list <- vector("list", length = length(samples))

for (i in seq_along(samples)) {

  samples_list[[i]] <- CreateSeuratObject(raw.data = samples.data[i]))

}

names(samples_list) <- samples



samples_list2 <- lapply(samples.data, CreateSeuratObject)

names(samples_list2) <- samples





share|improve this answer



















  • 1





    Thank you! I ended up going with lapply.

    – GLee
    Nov 15 '18 at 19:25
















0














Here are three ways of doing what you want. I suggest you do not use the first way.



samples <- c("a1", "a2", "a3")

samples.data <- c("a1.data", "a2.data", "a3.data")



for (i in seq_along(samples)) {

    assign(samples[i], CreateSeuratObject(raw.data = samples.data[i]))

}



samples_list <- vector("list", length = length(samples))

for (i in seq_along(samples)) {

  samples_list[[i]] <- CreateSeuratObject(raw.data = samples.data[i]))

}

names(samples_list) <- samples



samples_list2 <- lapply(samples.data, CreateSeuratObject)

names(samples_list2) <- samples





share|improve this answer



















  • 1





    Thank you! I ended up going with lapply.

    – GLee
    Nov 15 '18 at 19:25














0












0








0







Here are three ways of doing what you want. I suggest you do not use the first way.



samples <- c("a1", "a2", "a3")

samples.data <- c("a1.data", "a2.data", "a3.data")



for (i in seq_along(samples)) {

    assign(samples[i], CreateSeuratObject(raw.data = samples.data[i]))

}



samples_list <- vector("list", length = length(samples))

for (i in seq_along(samples)) {

  samples_list[[i]] <- CreateSeuratObject(raw.data = samples.data[i]))

}

names(samples_list) <- samples



samples_list2 <- lapply(samples.data, CreateSeuratObject)

names(samples_list2) <- samples





share|improve this answer













Here are three ways of doing what you want. I suggest you do not use the first way.



samples <- c("a1", "a2", "a3")

samples.data <- c("a1.data", "a2.data", "a3.data")



for (i in seq_along(samples)) {

    assign(samples[i], CreateSeuratObject(raw.data = samples.data[i]))

}



samples_list <- vector("list", length = length(samples))

for (i in seq_along(samples)) {

  samples_list[[i]] <- CreateSeuratObject(raw.data = samples.data[i]))

}

names(samples_list) <- samples



samples_list2 <- lapply(samples.data, CreateSeuratObject)

names(samples_list2) <- samples






share|improve this answer












share|improve this answer



share|improve this answer










answered Nov 15 '18 at 7:10









Rui BarradasRui Barradas

17.5k51731




17.5k51731








  • 1





    Thank you! I ended up going with lapply.

    – GLee
    Nov 15 '18 at 19:25














  • 1





    Thank you! I ended up going with lapply.

    – GLee
    Nov 15 '18 at 19:25








1




1





Thank you! I ended up going with lapply.

– GLee
Nov 15 '18 at 19:25





Thank you! I ended up going with lapply.

– GLee
Nov 15 '18 at 19:25




















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