Pathway analysis Run clusterProfiler on pathways provided by NCBI Biosytems to perform ORA or MSEA

Pathway analysis Run clusterProfiler on pathways provided by NCBI Biosytems to perform ORA or MSEA

pathway_analysis(
  in_list = NULL,
  universe = NULL,
  type = c("ora", "msea"),
  tax_id = 9606,
  include_general_pathways = FALSE,
  pvalueCutoff = 1,
  pAdjustMethod = "BH",
  minGSSize = 10,
  maxGSSize = 500,
  qvalueCutoff = 1,
  TERM2METAB = NULL,
  TERM2NAME = NULL,
  nPerm = 1000,
  verbose = TRUE,
  msea_by = "fgsea",
  seed = FALSE,
  exponent = 1
)

Arguments

in_list

a vector of metabolite id for ORA or a ranked named vector with scores for MSEA, where names are metabolite ids

universe

the set of all metabolites, required by ORA

type

"ora" or "msea"

tax_id

tax id

include_general_pathways

whether to include general pathways or not

pvalueCutoff

p-value cutoff

pAdjustMethod

p-value adjustment method

minGSSize

minimum metabolite set size

maxGSSize

maximum metabolite set size

qvalueCutoff

q-value cutoff

TERM2METAB

2-columns data.frame of pathways and metabolites

TERM2NAME

2-columns data.frame of pathways and pathway names

nPerm

number of permutations

verbose

verbose mode

msea_by

msea type

seed

set the seed

exponent

exponent in the msea approach

Value

A list with two elements

• res: gseaResult object or an enrichResult instance

• term_annotation: data.frame with pathway annotation