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To reference or cite the objects present in the Software Heritage archive, permalinks based on SoftWare Hash IDentifiers (SWHIDs) must be used.
Select below a type of object currently browsed in order to display its associated SWHID and permalink.

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swh:1:cnt:2a18c530457414123982ac65853d5cc9d90e238f
Citations

This interface enables to generate software citations, provided that the root directory of browsed objects contains a citation.cff or codemeta.json file.
Select below a type of object currently browsed in order to generate citations for them.

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Generate software citation in BibTex format (requires biblatex-software package)
Generating citation ...
#' K-means clusterisation.
#'
#' \code{performKmeans} returns a vector of corresponding clusters for
#'     each gene from a given ExpressionSet.
#'
#' @param es ExpressionSet object.
#'
#' @param columns List of specified columns' indices (optional), indices start from 0
#'
#' @param rows List of specified rows' indices (optional), indices start from 0
#'
#' @param k Expected number of clusters.
#'
#' @param replacena Method for replacing NA values
#'     in series matrix (mean by default)
#'
#' @return Vector of corresponding clusters, serialized to JSON.
#'
#' @import Biobase
#'
#' @examples
#' \dontrun{
#' data(es)
#' performKmeans(es, k = 2)
#' }
performKmeans <- function(es, columns = c(), rows = c(), k,
                            replacena = "mean") {
    assertthat::assert_that(k > 0)

    es <- subsetES(es, columns=columns, rows=rows)

    scaledExprs <- unname(t(scale(t(exprs(es)))))



    naInd <- which(is.na(scaledExprs), arr.ind = TRUE)
    if (nrow(naInd) > 0) {
        replaceValues <- apply(scaledExprs, 1, replacena, na.rm=TRUE)
        scaledExprs[naInd] <- replaceValues[naInd[,1]]
        rowsToCluster <- is.finite(replaceValues)
    } else {
        rowsToCluster <- seq_len(nrow(scaledExprs))
    }

    km <- stats::kmeans(scaledExprs[rowsToCluster, ], k, iter.max = 100L)
    res <- character(nrow(scaledExprs))
    res[rowsToCluster] <- as.character(km$cluster)
    return(jsonlite::toJSON(res))
}

Software Heritage — Copyright (C) 2015–2025, The Software Heritage developers. License: GNU AGPLv3+.
The source code of Software Heritage itself is available on our development forge.
The source code files archived by Software Heritage are available under their own copyright and licenses.
Terms of use: Archive access, API— Contact— JavaScript license information— Web API

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