Integrate proteomics data into Seurat object

[nithyabioinfo]

When attempting to reproduce the results, I encountered an issue at the integration step.

combined <- panc_pept_batch$corrected data %>%
as.data.frame() %>%
rownames_to_column(var = "Modified.Sequence") %>%
pivot_longer(-Modified.Sequence,
names_to = "SampleID",
values_to = "Intensity") %>%
full_join(.,meta) %>%
dplyr::select(SampleID,Assigned.Modifications, Modified.Sequence, Protein.ID, Gene, Intensity) %>%
mutate(Protein = case_when(Gene == "" ~ Protein.ID,
TRUE ~ Gene)) %>%
distinct(Protein, Modified.Sequence, SampleID, Intensity) %>%
dplyr::rename(protein_list = Protein,
sample_list = SampleID,
id = Modified.Sequence,
quant = Intensity) %>%
filter(!is.na(quant)) %>%
as.list() %>%
iq::fast_MaxLFQ(.) %>%
.[[1]]

The error is attached below,

Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'as.list': object 'meta' not found
Calls: %>% ... same_src.data.frame -> is.data.frame -> .handleSimpleError -> h
Execution halted.
Help to solve this issue.

[Cajun-data]

Hello @nithyabioinfo , the issue appears to be the meta object is missing. I believe this section of code came from lines 131-152 in 'Seurat_Correlations_MarkerProteins.R" - yes? If so, ensure line 101 was run to generate the "meta" object.

meta <- panc_pept[c(2,9,10,11,13)]