patch_annotation: fix missing gene types in annotation file
In olobiolo/siscreenr: Analyze Genome-Wide siRNA Screening Campaigns

Description Usage Arguments Details Value

Patch errors in annotation that escaped retry.

1	patch_annotation(x)

`x`	`data.frame` or path to file readable by `fread`

Even though update_annotation uses retry to alleviate random errors that occur when calling efetch in bulk, some queries still return errors. These will manifest as a "failed to retrieve" value in gene_type.

This function extracts the erroneous rows from a file or table, saves them to a temporary file in the current working directory, and runs update_annotation on that file. The fixed rows replace the bad ones in the original table and the fixed talbe is returned.

Once called, will run recursively until no errors are left. Will throw a warning if there are many errors to fix.

The annotation table with all bad rows fixed.

olobiolo/siscreenr documentation built on Nov. 26, 2021, 3:08 p.m.