Question: Enrichr : how to provide background as gene symbols or int ?
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gravatar for fr
7 months ago by
fr100
fr100 wrote:

I am using enrichr to perform some enrichment analyses. In their documentation they say that you can indicate the background list, or simply a number of genes for the background:

background (int) – BioMart dataset name for retrieving background gene information. This argument only works when gene_sets input is a gmt file or python dict. You could also specify a number by yourself, e.g. total expressed genes number. In this case, you will skip retrieving background infos from biomart.

source: https://gseapy.readthedocs.io/en/latest/run.html?highlight=background#gseapy.enrichr

  1. Is it possible to provide this background as human gene symbols? If so, how?
  2. May I provide the background myself? I want to have a smaller set of genes as background.
  3. I'm unable to provide the size for the background as well, and even though I have background=700, I still get ValueError: backgroud should be set or int object

thanks in advance

gsea rna-seq microarray gene • 381 views
ADD COMMENTlink modified 7 months ago • written 7 months ago by fr100
1
gravatar for fr
7 months ago by
fr100
fr100 wrote:

1. Is it possible to provide this background as human gene symbols? If so, how?

Writing background=hsapiens_gene_ensembl allows to use gene symbols, not only ensembl ids.

2. May I provide the background myself? I want to have a smaller set of genes as background.

The latest commit (version 0.9.10) seems to allow for this, but I was unable to implement it myself. See commit

3. I'm unable to provide the size for the background as well, and even though I have background=700, I still get ValueError: backgroud should be set or int object.

The latest commit (version 0.9.10) solves this issue.

ADD COMMENTlink modified 7 months ago • written 7 months ago by fr100
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