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FindMarkers fc.name does not yield the expected output #4474

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igordot opened this issue May 14, 2021 · 1 comment
Closed

FindMarkers fc.name does not yield the expected output #4474

igordot opened this issue May 14, 2021 · 1 comment
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@igordot
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igordot commented May 14, 2021

I tried using the FindMarkers() or FindAllMarkers() fc.name parameter in Seurat 4.0.1, but it does not seem to have any effect:

> library(Seurat)
Attaching SeuratObject
> data("pbmc_small")
> markers <- FindMarkers(object = pbmc_small, ident.1 = 2, fc.name = "xxx")
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
> head(markers)
                p_val avg_log2FC pct.1 pct.2    p_val_adj
HLA-DPB1 2.667056e-08   2.523409 0.947 0.410 6.134228e-06
MS4A1    7.532290e-08   6.540876 0.526 0.033 1.732427e-05
HLA-DQB1 2.436852e-07   2.956945 0.789 0.246 5.604759e-05
HLA-DRB1 1.341885e-06   2.393562 0.842 0.410 3.086335e-04
HLA-DRA  4.618445e-06   2.614768 0.895 0.623 1.062242e-03
TCL1A    6.943137e-06   5.886009 0.368 0.016 1.596922e-03

The fold change column in still avg_log2FC. Is this expected behavior?
@igordot igordot added the bug Something isn't working label May 14, 2021
timoast added a commit that referenced this issue May 14, 2021
@timoast
Pass fc.name parameter; #4474
7cd62d6
@timoast
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timoast commented May 14, 2021

This should now be fixed on the develop branch

@timoast timoast closed this as completed May 14, 2021
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@timoast @igordot