Use a custom gene set?

[heinin]

Is it possible to use a custom gene set to calculate the enrichment scores?

[guokai8]

Hi @heinin, I am not sure your "custom gene set" looks like? maybe a matrix? Yes, it supports; a vector ? No. Or "custom gene set" mean the annotation file? Yes, it supports. K

[saeedfc]

Thank you for developing this package. As of now, it looks like I have to build an annotation object which is restricted to few databases. Sometimes, i want to run custom gene sets as mentioned above. This can be made into a data frame where I have a column for genes and a second column for Function/Annotation. Another way could be as named lists or GMT files. Will it be possible to build an annotation object from a custom gene set like that to be used with scGSVA?

Thanks, Saeed

[guokai8]

Hi @saeedfc, You can use the annotation file with a dataframe (first column is the gene name, second column is the Function or Annotation). Please try it and then let me know if you have any issues. And if you want to have a annotation object, you can use my bioAnno (https://github.com/guokai8/bioAnno) package with the fromOwn function. K

[saeedfc]

Thanks, it works. However, it needs 3 columns in the annotation data frame. 1st for genes and 3rd for annotation of the genes.

[guokai8]

Hi @saeedfc, Please set useTerm=F, if you just have two columns. K

[guokai8]

Hi @saeedfc , please install the newest version. K