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
asked Nov 15 '18 at 6:36
GLeeGLee
32
add a comment |
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
asked Nov 15 '18 at 6:36
GLeeGLee
32
This is a bad idea. 1) You are rewritingievery time through the inner loop onj. 2) You are trying to createn = length(samples)objects in the global environment. Instead you should keep the objects in alist.
– Rui Barradas
Nov 15 '18 at 7:04
add a comment |
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
asked Nov 15 '18 at 6:36
GLeeGLee
32
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
asked Nov 15 '18 at 6:36
GLeeGLee
32
asked Nov 15 '18 at 6:36
GLeeGLee
32
asked Nov 15 '18 at 6:36
GLeeGLee
32
asked Nov 15 '18 at 6:36
GLeeGLee
32
asked Nov 15 '18 at 6:36
GLeeGLee
32
32
This is a bad idea. 1) You are rewritingievery time through the inner loop onj. 2) You are trying to createn = length(samples)objects in the global environment. Instead you should keep the objects in alist.
– Rui Barradas
Nov 15 '18 at 7:04
add a comment |
This is a bad idea. 1) You are rewritingievery time through the inner loop onj. 2) You are trying to createn = length(samples)objects in the global environment. Instead you should keep the objects in alist.
– 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
add a comment |
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
answered Nov 15 '18 at 7:10
Rui BarradasRui Barradas
17.5k51731
1
Thank you! I ended up going with lapply.
– GLee
Nov 15 '18 at 19:25
add a comment |
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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
answered Nov 15 '18 at 7:10
Rui BarradasRui Barradas
17.5k51731
1
Thank you! I ended up going with lapply.
– GLee
Nov 15 '18 at 19:25
add a comment |
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
answered Nov 15 '18 at 7:10
Rui BarradasRui Barradas
17.5k51731
1
Thank you! I ended up going with lapply.
– GLee
Nov 15 '18 at 19:25
add a comment |
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
answered Nov 15 '18 at 7:10
Rui BarradasRui Barradas
17.5k51731
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
answered Nov 15 '18 at 7:10
Rui BarradasRui Barradas
17.5k51731
answered Nov 15 '18 at 7:10
Rui BarradasRui Barradas
17.5k51731
answered Nov 15 '18 at 7:10
Rui BarradasRui Barradas
17.5k51731
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
add a comment |
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
add a comment |
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This is a bad idea. 1) You are rewriting
ievery time through the inner loop onj. 2) You are trying to createn = length(samples)objects in the global environment. Instead you should keep the objects in alist.– Rui Barradas
Nov 15 '18 at 7:04