User: Pratik Mehta

gravatar for Pratik Mehta
Pratik Mehta30
Reputation:
30
Status:
New User
Location:
University of Connecticut
Last seen:
7 hours ago
Joined:
2 months ago
Email:
p************@gmail.com

Posts by Pratik Mehta

<prev • 24 results • page 1 of 3 • next >
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What format should a dataframe be in to use the AddMetaData function in Seurat?
... I've been having trouble with this. I can directly cbind the dataframe to Seurat using the commands in this post: https://www.biostars.org/p/460935/#461095 However, I want to use the built in Seurat function `AddMetaData`. Any clues? ...
scrna-seq R seurat rna-seq written 3 days ago by Pratik Mehta30
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Comment: C: How to read a dataframe into Seurat for AddMetaData properly?
... Instead of cell barcode, the cells are labeled by the unique cell sample name, that's all. I was wondering what format a data frame should be in, in order to use it to add meta data using the `AddMetaData` function. ...
written 24 days ago by Pratik Mehta30
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Comment: C: How to read a dataframe into Seurat for AddMetaData properly?
... That worked with scfp <- AddMetaData, Gosh, silly mistake... but now problem is the MetaData displays as NA NA NA NA NA... I think it could be a problem with how my dataframe is formatted, and the way Seurat wants it. swbarnes2, if you don't mind me asking when you're loading a data frame what do ...
written 26 days ago by Pratik Mehta30
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How to read a dataframe into Seurat for AddMetaData properly?
... Before I report this as a bug can someone show me the proper way to add metadata using the `AddMetaData` function. I first read a file that is new line delimited with the meta data labels I want using read table. The ftimecell_columns.txt file looks like this: "12wks" "12wks" "12wks" ...
R seurat rna-seq written 27 days ago by Pratik Mehta30 • updated 26 days ago by swbarnes28.8k
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Comment: C: How to embed known cell information into Seurat object? AddMetaData?
... I understand, I would, but it didn't work for me : ( EDIT: I think I'll report it as a bug? ...
written 27 days ago by Pratik Mehta30
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Comment: C: How to embed known cell information into Seurat object? AddMetaData?
... I double checked the order prior to cbinding on of the Seurat object by doing `> head(x = scfp@meta.data)` I would simply do `AddMetaData`, but it did not work for me, unfortunately. There was no error message. It just didn't show up under the Seurat object. The method above, however, did work ...
written 27 days ago by Pratik Mehta30
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Comment: C: How to embed known cell information into Seurat object? AddMetaData?
... So I tried the AddMetaData way by doing: AddMetaData(object = scfp, metadata = celltypes_col, col.name = 'time.cell') But that did not work! What you suggested, igor, helped, treating the `seurat_obj@meta.data` as a data frame. I was able to add the meta data using this: scfp@meta.data & ...
written 5 weeks ago by Pratik Mehta30
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Comment: C: How to embed known cell information into Seurat object? AddMetaData?
... Wow, this is incredibly helpful. I will keep this bookmarked, and attempt this method soon! Thank you Thank you swbarnes2! ...
written 5 weeks ago by Pratik Mehta30
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Comment: C: How to embed known cell information into Seurat object? AddMetaData?
... Gosh, thank you Hamid! I am going to try this soon! I will let you know how I make out! ...
written 5 weeks ago by Pratik Mehta30
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How to embed known cell information into Seurat object? AddMetaData?
... How to embed known cell information into Seurat object? Using AddMetaData? Is this possible? I read this documentation: https://www.rdocumentation.org/packages/Seurat/versions/3.1.4/topics/AddMetaData However I need some clarification on how to go about doing this, please? I have cell labels tha ...
scrna-seq R next-gen seurat3 written 5 weeks ago by Pratik Mehta30 • updated 5 weeks ago by swbarnes28.8k

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