DecoupleR integration

2024-02-27

We provide wrapper functions to spatially quantify Pathway and Transcription Factor activities using DecoupleR.

library(spacedeconv)

## → checking spacedeconv environment and dependencies

library(decoupleR)

To compute activities you need to obtain a reference from OmniPathR. The method can be one of “progeny”, “dorothea” or “collectri”.

ref <- get_decoupleR_reference(method = "progeny", organism = "human")
## ── spacedeconv ─────────────────────────────────────────────────────────────────
## ℹ Getting decoupleR reference
## Warning in OmnipathR::get_annotation_resources(): 'OmnipathR::get_annotation_resources' is deprecated.
## Use 'annotation_resources' instead.
## See help("Deprecated")
## Warning in OmnipathR::import_omnipath_annotations(resources = name, ..., : 'OmnipathR::import_omnipath_annotations' is deprecated.
## Use 'annotations' instead.
## See help("Deprecated")
## ✔ Got decoupleR reference [39.6s]
## 
head(ref)
## # A tibble: 6 × 4
##   source   target  weight  p_value
##   <chr>    <chr>    <dbl>    <dbl>
## 1 Androgen TMPRSS2  11.5  2.38e-47
## 2 Androgen NKX3-1   10.6  2.21e-44
## 3 Androgen MBOAT2   10.5  4.63e-44
## 4 Androgen KLK2     10.2  1.94e-40
## 5 Androgen SARG     11.4  2.79e-40
## 6 Androgen SLC38A4   7.36 1.25e-39

In the next step the activities can be computed.

data("spatial_data_3")
spatial_data_3 <- preprocess(spatial_data_3)
spatial_data_3 <- normalize(spatial_data_3)

spe <- compute_activities(spatial_data_3, reference = ref, method = "wmean", assay = "cpm")