About scape

[lancy-liang]

Hi, Ran.
I used psiCategory.R to calculate the psi values for pA sites, but I thought it would calculate the psi values for genes. In your article, "Category of pA usage" mentions, "To better understand the heterogeneity of APA patterns among cell populations, we first calculated the usage of pA sites for each gene at single cell level." Is this categorization for genes or for pA sites?
Regarding the section on "Expected pA length," is the calculated value referring to the usage of a single pA site or the usage of pA sites within a gene?
thank you very much!

[zhou-ran]

Hi lancy,

The category perteins to pA sites, determined by the psi value of the pA site within a gene. In contrast, the expected pA length is linked to a gene. Specifically, we compute an expected length for pA sites located in the 3'UTR of a gene.

Ran

[lancy-liang]

Hi,ran
Thank you very much for your answer.
I used the scape.R code you provided, but it seems that I didn't get the Expected pA length of the gene.Do I need to calculate the Expected pA length by myself? If possible, can you share the code to calculate the expected pA length of the gene?
thank you very much!!
lancy