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BAUDOTlab / scDataPipeline

Reusable standard single-cell RNA sequencing data analysis pipeline
MIT License
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Add error handling for genes_of_interest file in 05_annotDEAviz_pipeline #50

Closed PhilippeBaratta closed 8 months ago

PhilippeBaratta commented 10 months ago

This commit introduces a "try-catch" in 05_annotDEAviz_pipeline.Rmd to handle various formats of the genes_of_interest file. It first attempts to read the file with default settings and, if that fails, tries reading with specified comma separator and column classes.

Rumengol commented 10 months ago

I'm not completely sure what the file would look like in the alternative format, can you provide an example?

PhilippeBaratta commented 8 months ago

I'm using a file located at '/home/philippeb/single_cell_embryo_E9/01_requirements/genes_of_interest3-scRNAseq.tsv'. Initially, the command to read this file failed. To address this issue, I attempted to account for the potential presence of a comma (',') as a separator in the file. This adjustment was made using a try-catch method, ensuring that the reading process can handle unexpected errors without disrupting normal use.