WebGestaltRMultiOmics: WebGestaltRMultiOmics
In bzhanglab/WebGestaltR: Gene Set Analysis Toolkit WebGestaltR

WebGestaltRMultiOmics

R Documentation

WebGestaltRMultiOmics

Description

Perform multi-omics analysis using WebGestaltR

Usage

WebGestaltRMultiOmics(
  analyteLists = NULL,
  analyteListFiles = NULL,
  analyteTypes = NULL,
  enrichMethod = "ORA",
  organism = "hsapiens",
  enrichDatabase = NULL,
  enrichDatabaseFile = NULL,
  enrichDatabaseType = NULL,
  enrichDatabaseDescriptionFile = NULL,
  collapseMethod = "mean",
  minNum = 10,
  maxNum = 500,
  fdrMethod = "BH",
  sigMethod = "fdr",
  fdrThr = 0.05,
  topThr = 10,
  reportNum = 100,
  setCoverNum = 10,
  perNum = 1000,
  gseaP = 1,
  isOutput = TRUE,
  outputDirectory = getwd(),
  projectName = NULL,
  dagColor = "binary",
  saveRawGseaResult = FALSE,
  gseaPlotFormat = "png",
  nThreads = 1,
  cache = NULL,
  hostName = "https://www.webgestalt.org/",
  useWeightedSetCover = TRUE,
  useAffinityPropagation = FALSE,
  usekMedoid = FALSE,
  kMedoid_k = 25,
  isMetaAnalysis = TRUE,
  mergeMethod = "mean",
  normalizationMethod = "rank",
  referenceLists = NULL,
  referenceListFiles = NULL,
  referenceTypes = NULL,
  referenceSets = NULL,
  listNames = NULL
)

Arguments

`analyteLists`	`vector` of the ID type of the corresponding interesting analyte list. The supported ID types of WebGestaltR for the selected organism can be found by the function `listIdType`. If the `organism` is `others`, users do not need to set this parameter. The length of `analyteLists` should be the same as the length of `analyteListFiles` or `analyteLists`.
`analyteListFiles`	If `enrichMethod` is `ORA`, the extension of the `analyteListFiles` should be `txt` and each file can only contain one column: the interesting analyte list. If `enrichMethod` is `GSEA`, the extension of the `analyteListFiles` should be `rnk` and the files should contain two columns separated by tab: the analyte list and the corresponding scores.
`analyteTypes`	a vector containing the ID types of the analyte lists.
`enrichMethod`	Enrichment methods: `ORA`or `GSEA`.
`organism`	Currently, WebGestaltR supports 12 organisms. Users can use the function `listOrganism` to check available organisms. Users can also input `others` to perform the enrichment analysis for other organisms not supported by WebGestaltR. For other organisms, users need to provide the functional categories, interesting list and reference list (for ORA method). Because WebGestaltR does not perform the ID mapping for the other organisms, the above data should have the same ID type.
`enrichDatabase`	The functional categories for the enrichment analysis. Users can use the function `listGeneSet` to check the available functional databases for the selected organism. Multiple databases in a vector are supported for ORA and GSEA.
`enrichDatabaseFile`	Users can provide one or more GMT files as the functional category for enrichment analysis. The extension of the file should be `gmt` and the first column of the file is the category ID, the second one is the external link for the category. Genes annotated to the category are from the third column. All columns are separated by tabs. The GMT files will be combined with `enrichDatabase`.
`enrichDatabaseType`	The ID type of the genes in the `enrichDatabaseFile`. If users set `organism` as `others`, users do not need to set this ID type because WebGestaltR will not perform ID mapping for other organisms. The supported ID types of WebGestaltR for the selected organism can be found by the function `listIdType`.
`enrichDatabaseDescriptionFile`	Users can also provide description files for the custom `enrichDatabaseFile`. The extension of the description file should be `des`. The description file contains two columns: the first column is the category ID that should be exactly the same as the category ID in the custom `enrichDatabaseFile` and the second column is the description of the category. All columns are separated by tabs.
`collapseMethod`	The method to collapse duplicate IDs with scores. `mean`, `median`, `min` and `max` represent the mean, median, minimum and maximum of scores for the duplicate IDs.
`minNum`	WebGestaltR will exclude the categories with the number of annotated genes less than `minNum` for enrichment analysis. The default is `10`.
`maxNum`	WebGestaltR will exclude the categories with the number of annotated genes larger than `maxNum` for enrichment analysis. The default is `500`.
`fdrMethod`	For the ORA method, WebGestaltR supports five FDR methods: `holm`, `hochberg`, `hommel`, `bonferroni`, `BH` and `BY`. The default is `BH`.
`sigMethod`	Two methods of significance are available in WebGestaltR: `fdr` and `top`. `fdr` means the enriched categories are identified based on the FDR and `top` means all categories are ranked based on FDR and then select top categories as the enriched categories. The default is `fdr`.
`fdrThr`	The significant threshold for the `fdr` method. The default is `0.05`.
`topThr`	The threshold for the `top` method. The default is `10`.
`reportNum`	The number of enriched categories visualized in the final report. The default is `20`. A larger `reportNum` may be slow to render in the report.
`setCoverNum`	The number of expected gene sets after set cover to reduce redundancy. It could get fewer sets if the coverage reaches 100%. The default is `10`.
`perNum`	The number of permutations for the GSEA method. The default is `1000`.
`gseaP`	The exponential scaling factor of the phenotype score. The default is `1`. When p=0, ES reduces to standard K-S statistics (See original paper for more details).
`isOutput`	If `isOutput` is TRUE, WebGestaltR will create a folder named by the `projectName` and save the results in the folder. Otherwise, WebGestaltR will only return an R `data.frame` object containing the enrichment results. If hundreds of gene list need to be analyzed simultaneously, it is better to set `isOutput` to `FALSE`. The default is `TRUE`.
`outputDirectory`	The output directory for the results.
`projectName`	The name of the project. If `projectName` is `NULL`, WebGestaltR will use time stamp as the project name.
`dagColor`	If `dagColor` is `binary`, the significant terms in the DAG structure will be colored by steel blue for ORA method or steel blue (positive related) and dark orange (negative related) for GSEA method. If `dagColor` is `continous`, the significant terms in the DAG structure will be colored by the color gradient based on corresponding FDRs.
`saveRawGseaResult`	Whether the raw result from GSEA is saved as a RDS file, which can be used for plotting. Defaults to `FALSE`. The list includes Enrichment_Results A data frame of GSEA results with statistics Running_Sums A matrix of running sum of scores for each gene set Items_in_Set A list with ranks of genes for each gene set
`gseaPlotFormat`	The graphic format of GSEA enrichment plots. Either `svg`, `png`, or `c("png", "svg")` (default).
`nThreads`	The number of cores to use for GSEA and set cover, and in batch function.
`cache`	A directory to save data cache for reuse. Defaults to `NULL` and disabled.
`hostName`	The server URL for accessing data. Mostly for development purposes.
`useWeightedSetCover`	Use weighted set cover for ORA. Defaults to `TRUE`.
`useAffinityPropagation`	Use affinity propagation for ORA. Defaults to `FALSE`.
`usekMedoid`	Use k-medoid for ORA. Defaults to `TRUE`.
`kMedoid_k`	The number of clusters for k-medoid. Defaults to `25`.
`isMetaAnalysis`	whether to perform meta-analysis. Defaults to `TRUE`. FALSE is not currently implemented.
`mergeMethod`	The method to merge the results from multiple omics (options: `mean`, `max`). Only used if `isMetaAnalysis = FALSE`. Defaults to `mean`.
`normalizationMethod`	The method to normalize the results from multiple omics (options: `rank`, `median`, `mean`). Only used if `isMetaAnalysis = FALSE`.
`referenceLists`	For the ORA method, users can also use an R object as the reference gene list. `referenceLists` should be an R `vector` object containing the reference gene list.
`referenceListFiles`	For the ORA method, the users need to upload the reference gene list. The extension of the `referenceListFile` should be `txt` and the file can only contain one column: the reference gene list.
`referenceTypes`	Vector of the ID types of the reference lists. The supported ID types of WebGestaltR for the selected organism can be found by the function `listIdType`. If the `organism` is `others`, users do not need to set this parameter.
`referenceSets`	Users can directly select the reference sets from existing platforms in WebGestaltR and do not need to provide the reference set through `referenceListFiles`. All existing platforms supported in WebGestaltR can be found by the function `listReferenceSets`. If `referenceListFiles` and `refereneceLists` are `NULL`, WebGestaltR will use the `referenceSets` as the reference analyte sets. Otherwise, WebGestaltR will use the user supplied reference set for enrichment analysis. Must be a vector with length matching the input analyte list (i.e. c('genome', 'genome', 'KEGG'))
`listNames`	The names of the analyte lists.