scRNA seq with seurat: how do I add a column to the metadata?
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23 months ago
cdeantoneo31 ▴ 20

I am trying to analyze the data from a paper, and was presented with an mtx file, barcode.tsv, and genes.tsv. i can successfully add these into R as a seurat object, but instead of doing clustering myself I would like to use a txt file that was uploaded along with these other files, which seems to include their clustering and the coordinates for a umap

the txt is below

                      cluster   CellType    condition   HashAssignment  UMAP_1  UMAP_2
AAACCCAAGAGCAAGA-1_1    3   Fibroblast  WT  B0308   -1.40413515808334   4.42566178583769
AAACCCACATCTGCGG-1_1    1   Immune  WT  B0308   3.24737412688981    -8.88317419743868
AAACCCATCGATGCAT-1_1    0   Fibroblast  WT  B0309   -2.68064873459091   3.80931518816618
AAACGAACAACTCCAA-1_1    3   Fibroblast  WT  B0310   2.87252790687333    5.71203921579984
AAACGAACAGCTGGTC-1_1    5   Fibroblast  WT  B0306   -4.88596980812301   3.06808994555143
AAACGAATCAGCGGAA-1_1    0   Fibroblast  WT  B0307   -3.71260421516647   8.08994601511625
AAACGAATCCTGGGAC-1_1    0   Fibroblast  WT  B0307   -3.86652391197433   7.87874720835355

However, I cannot figure out how to do this. It seems like the best way would be to add the information to the mtx meta. Am I on the right track, and if so how would I go about doing this?

The only thing I can think of is to add the cluster

scRNA-seq scRNA • 968 views
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You can use obj@meta.data to reference the metadata data frame directly, so obj@meta.data$myclust <- read.csv('myclust.csv')$cluster may do the trick -- so long as the file has exactly the same number of cells in exactly the same order as the barcode.tsv file.

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