create_module_bf: create a module based on provided biological features

In onertipaday/rcompass: R Client for the COMPASS GrapgQL API

Description

create a module based on provided biological features

Usage

create_module_bf(
  compendium = "vespucci",
  biofeaturesNames = NULL,
  normalization = "limma",
  rank = "magnitude",
  top_n = 50,
  sorted = FALSE,
  useIds = FALSE
)

Arguments

compendium	A string - the selected compendium
biofeaturesNames	A character vector (gene_names)
normalization	A string - either 'limma' (default),'tpm' or legacy as normalization
rank	A string ('magnitude' as default)
top_n	A numeric - an integer for selecting the top ranked samplesets
sorted	A logical (FALSE as default) - it returns a sorted index for both bf and ss
useIds	A logical (FALSE as default) - It allows using biofeatureIds

Value

A SummarizedExperiment object

Examples

## Not run: 
my_bf <- c("VIT_00s0246g00220","VIT_00s0332g00060","VIT_00s0332g00110")
tmp <- get_biofeature_id(id_In = my_bf, useIds = F)$id
my_mod <- create_module_bf(biofeaturesNames= tmp,
normalization = "limma", top_n = 15, useIds = T)

## End(Not run)

onertipaday/rcompass documentation built on Sept. 18, 2021, 5:13 p.m.