Iterate through Seurat object to add patient information

Question

[kousi31]

I want to add patient information to individual Seurat objects before merging them. I have a the patient characteristics as dataframe named covid-19

Adding info to individual obj as below works,

cov01 <- AddMetaData(cov01, metadata = c(covid_19[1,]), col.name =
colnames(covid_19))

However, when I I try to use forloop to automate, I am getting an error.

Error in UseMethod(generic = "AddMetaData", object = object) : 
no applicable method for 'AddMetaData' applied to an object of class "list"

S_obj = c(cov01, cov02, cov03, cov04, cov07, cov08, cov09, cov10, cov11, cov12, cov17, cov18) # name of my Seurat objects

for (i in 1:12) {
  S_obj[i] <- AddMetaData(S_obj[i], metadata = c(covid_19[i,]), col.name = colnames(covid_19))
}

How to iterate through Seurat objects?

[Ram]

What is the output to class(S_obj[1])? Also, try using as.vector(covid_19[i]) instead of c(covid_19[i,]).

[kousi31]

> class(S_obj[1])
[1] "list"

> class(S_obj[[1]])
[1] "Seurat"
attr(,"package")
[1] "SeuratObject"

When I run the loop with two square brackets S_obj[[i]], it runs without taking the object name and without throwing error. When I check the metadata the patient info is not added.

> S_obj = c(cov01, cov02, cov03, cov04, cov07, cov08, cov09, cov10, cov11, cov12, cov17, cov18)
> 
> for (i in 1:12) {
+ 
+ S_obj[[i]] <- AddMetaData(S_obj[[i]], metadata = c(covid_19[i,]), col.name = colnames(covid_19))
+ }
>   

[kousi31]

The problem is the forloop doesn't take the object name from the list during iteration

[Ram]

What do you mean by "object name"?

[Ram]

First off, ensure it works for one object before you run a loop. Change your code to this:

S_obj = c(cov01, cov02, cov03, cov04, cov07, cov08, cov09, cov10, cov11, cov12, cov17, cov18)


## Use `unlist` instead of `c`; the former makes the row a character vector, see the other code segment:
S_obj[[1]] <- AddMetaData(S_obj[[1]], metadata = unlist(covid_19[1,]), col.name = colnames(covid_19))

## Check S_obj[[1]] and make sure things are OK before running the code on ALL objects

for (i in 2:12) {
  S_obj[[i]] <- AddMetaData(S_obj[[i]], metadata = unlist(covid_19[i,]), col.name = colnames(covid_19))
}

How I picked unlist:

library(dplyr)
df <- tibble(Sample_id=c("cov01","cov02","cov03","cov04","cov07"),Age=c(73,53,75,59,84), Disease_status=c(rep("covid-19", times=4),"Healthy"), Disease_severity=c("Severe","Moderate","Moderate","Severe",NA), Days_since_symptom_onset=c(15,9,2,16,NA))

df
# A tibble: 5 × 5
  Sample_id   Age Disease_status Disease_severity Days_since_symptom_onset
  <chr>     <dbl> <chr>          <chr>                               <dbl>
1 cov01        73 covid-19       Severe                                 15
2 cov02        53 covid-19       Moderate                                9
3 cov03        75 covid-19       Moderate                                2
4 cov04        59 covid-19       Severe                                 16
5 cov07        84 Healthy        NA                                     NA

df[1,]
# A tibble: 1 × 5
  Sample_id   Age Disease_status Disease_severity Days_since_symptom_onset
  <chr>     <dbl> <chr>          <chr>                               <dbl>
1 cov01        73 covid-19       Severe                                 15

class(df[1,])
[1] "tbl_df"     "tbl"        "data.frame"

class(c(df[1,]))
[1] "list"

class(as.vector(df[1,]))
[1] "list"

class(unlist(df[1,]))
[1] "character"

unlist(df[1,])
               Sample_id                      Age           Disease_status         Disease_severity Days_since_symptom_onset
                 "cov01"                     "73"               "covid-19"                 "Severe"                     "15"

[kousi31]

By object name I mean the name I gave to Seurat objects for my individual samples (I have 12 'individuals' in the dataset).

The code works fine for individual samples, e.g.

cov01 <- AddMetaData(cov01, metadata = c(covid_19[1,]), col.name = colnames(covid_19))

However, the forloop doesn't iterate through the 12 Seurat objects.

If I run individually like this it works;

cov01 <- AddMetaData(cov01, metadata = c(covid_19[1,]), col.name = colnames(covid_19))
cov02 <- AddMetaData(cov02, metadata = c(covid_19[2,]), col.name = colnames(covid_19))
cov03 <- AddMetaData(cov03, metadata = c(covid_19[3,]), col.name = colnames(covid_19))
cov04 <- AddMetaData(cov04, metadata = c(covid_19[4,]), col.name = colnames(covid_19))

But the forloop doesn't.

[Ram]

I combined your comments into a single comment. Please note that "forloop" is not a thing, it's a for loop - 2 words.

Anyway, this is quite odd. Can I ask you try one last thing - use list() instead of c() to create the S_obj list.