workflow for ORA

workflow for ORA

runWebGestaltORA(
  data,
  fpath,
  organism = "hsapiens",
  ID_col = "UniprotID",
  target = "geneontology_Biological_Process",
  threshold = 0.59,
  greater = TRUE,
  nperm = 10,
  score_col = "estimate",
  outdir = "WebGestalt_ORA",
  subdir_name = NULL,
  interestGeneType = "uniprotswissprot",
  contrast_name = fpath
)

Arguments

data

data
fpath

file path to write to
organism

organism
ID_col

column name containing IDs
target

target database, default: "geneontology_Biological_Process"
threshold

threshold for estimate
greater

indicating direction of threshold
nperm

number of permutations
score_col

column name containing estimates
outdir

output directory
subdir_name

subdirectory name
interestGeneType

what type of identifier default : "uniprotswissprot"
contrast_name

default fpath