omePath: omics enrichment analysis

In omicsEye/deepath: Generic Omics Pathway Enrichment Analysis

omics enrichment analysis

Description

omics enrichment analysis

Usage

omePath(
  input_data,
  output = "output",
  mapper_file,
  pathway_col = "Pathway",
  feature_col = "Feature",
  input_metadata = NA,
  meta = NA,
  case_label = NA,
  control_label = NA,
  score_col = "logFC",
  pval_threshold = 0.05,
  fdr_threshold = NA,
  Pathway.Subject = NA,
  method = "ks",
  min_member = 2,
  do_plot = TRUE
)

Arguments

input_data	It could be either 1) a score file which has at least a column for feature names and an column for scores, or 2) a omics profile which has rows as samples and columns as features
output	output a directory path to where user wants resulst to be written
mapper_file	a mapping file that has at least towcolumns one for pathways and one for features in each pathways in long format
pathway_col	a column for pathways in the mapper_file
feature_col	a column for features in the mapper_file
input_metadata	a file or data frame that has metadata where score file in not provided and scores need to be calulated usig input_data, input_metadata, and meta
meta	a couln name in input_metadata when score needs to be calculated an d score file is not provided (input_data is not a core file but a omics profile)
case_label	a name for case group and is part of meta values.
control_label	a name for control group and is part of meta values.
score_col	a columnb name in input_data
pval_threshold	a threshold for p-value which will be used to decide to visualize result for a pathway or not
fdr_threshold	a threshold for fdr which will be used to decide to visualize result for a pathway or not
Pathway.Subject	a pathway subject when HMDB database is provided as reference for metabolites (as omics features)
method	a enrichment methods to be used, options are ks, gset, and wilcox
min_member	a condition for a pathway to be analyzed as minimum number of a pathway members to be seen in the study
do_plot	a TRUE or FALSE to plot result or not

Value

The result as a list of 1) 'enrichment_stats' a table for statistic of pathway enrichment, 'rank_plots' a list of ggplots for density plot of enrichment base don rank of features, and 3) 'score_plots' a list of ggplots for density plot of enrichment base don score of feature.

Examples

omePath_result <- omePath::omePath(input_data = score_data_no_COVID, input_metadata = NA, 
pathway_col = "Pathway", feature_col = "Feature", meta <- NA, case_label <- "", 
control_label <- "", output = "~/omePath_enrichment_metabolite_no_COVID_fdr1",
input_data = score_data_no_COVID,
score_col = 'coef', 
pval_threshold = 0.05, 
fdr_threshold = NA, 
Pathway.Subject = NA,#'Metabolic', 
do_plot = TRUE, 
mapper_file = "~/Databases/Metabolomics/Pathways/smpdb_metabolites.tsv",
method = "wilcox",
min_member = 2)

omicsEye/deepath documentation built on Nov. 6, 2023, 6:04 a.m.