How to remove entire rows from seurat object based on cellhash read

Question

[cook.675]

Heres the last 3 columns of metadata from my seurat object (pbs.hashtag):

                 hash.ID  percent.mt  stim
AAACCCAAGGAGAGGC    htag2   4.786380  VEH
AAACCCAAGTCTCTGA    htag3   6.642512  VEH
AAACCCAAGTTTCAGC  Doublet   2.559588  VEH
AAACCCACACAGTCAT Negative   4.982733  VEH
AAACCCACACGCGCAT    htag2   3.220281  VEH
AAACCCACACGGATCC    htag2   3.391841  VEH

I want to remove all rows from the object that have Doublet as the hash ID. Here's what I tried:

pbs.hashtag <- subset(pbs.hashtag, subset = [e-mail] != "Doublet")

it didn't work obvioulsy it says:

Error in FetchData(object = object, vars = expr.char[vars.use], cells = cells, : None of the requested variables were found:

Any ideas? I also tried meta.data$hash.ID in the subset line. Im pretty new to R and Seurat but I used to program some C 20 years ago so im getting back in the pool.

thanks!

[tushard1987]

Hello,

could you please explain how how to get this doublet tag in the metadata?

thanks in advance!

Tushar

[f.morgana]

Hi there,

I tried to remove certain rows in my dataset as well using this function.

                                   Sample donor organ sort method file is.TRA.p is.TRB.p is.TRA.np

FCAImmP7179369-AAACGGGTCTGTCAAG      6     3     0    1      0    2    FALSE    FALSE     FALSE
FCAImmP7179369-AAATGCCAGCTTATCG      6     3     0    1      0    2    FALSE    FALSE     FALSE
FCAImmP7179369-AACTCAGTCATTGCGA      6     3     0    1      0    2    FALSE    FALSE     FALSE
FCAImmP7179369-AAGCCGCAGTGTCCCG      6     3     0    1      0    2    FALSE    FALSE     FALSE
FCAImmP7179369-AAGTCTGCACAGCCCA      6     3     0    1      0    2    FALSE    FALSE     FALSE
FCAImmP7179369-ACACCGGGTTCCACGG      6     3     0    1      0    2    FALSE    FALSE     FALSE

To clarify, I would like to remove all rows with Sample number 30 and 31 with the following code:

treg <- subset(treg, subset = Sample != c("30", "31"))

When I type in dim(treg) and look at the dimensions, it seems to have worked as I seem to have removed 44 cells by doing this. However, when I type View([e-mail]) and scroll down, I still see the cells that I wanted to have removed in my data frame. Am I doing something wrong? Is there a way to double check whether I have performed this properly? Why are my unwanted rows still present in my meta.data?

Many thanks in advance, Florencia

Answer 1

[cook.675]

Guys I got it! DUHHHH

pbs.hashtag <- subset(pbs.hashtag, subset = hash.ID != "Doublet")