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zhanghao-njmu / SCP

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
https://zhanghao-njmu.github.io/SCP/
GNU General Public License v3.0
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AnnotateFeatures #158

Closed 1269376398 closed 11 months ago

1269376398 commented 11 months ago

data("pancreas_sub") DEGs <- pancreas_sub@tools$DEtest_CellType$AllMarkers_wilcox DEGs <- DEGs[with(DEGs, avg_log2FC > 1 & p_val_adj < 0.05), ] pancreas_sub <- AnnotateFeatures(pancreas_sub, species = "Mus_musculus", db = c("TF", "SP")) Species: Mus_musculus

Loading cached db: TF version:AnimalTFDB4 nterm:2 created:2023-09-07 10:54:23 Error in aggregate.data.frame(as.data.frame(x), ...) : no rows to aggregate

I want to learn how to solve this?

realzehuali commented 11 months ago

same issue

luan99kk commented 11 months ago

same issue

zhanghao-njmu commented 11 months ago

I'm sorry, this error occurred because an incorrect database name was used. SCP changed the name of the SP database to CSPA in version 0.5 to differentiate it from another surface protein database called Surfaceome. However, the readme file was not updated to reflect this change, resulting in the error.

I have already updated the readme file. Please replace "SP" with "CSPA" in your current code.

luan99kk commented 11 months ago

Thanks for your reply. Thank you for your hard work

realzehuali commented 11 months ago

Thanks for your reply. Thank you for your hard work