Kang_subset {distinct} | R Documentation

## Subset from the 'Kang18_8vs8()' object of the `muscData` package.

### Description

Subset from the 'Kang18_8vs8()' object of the `muscData` package.

### Arguments

`Kang_subset` | contains a `SingleCellExperiment` object, representing a subset of 6 samples (3 individuals observed across 2 conditions) and 100 genes selected from the 'Kang18_8vs8()' object of the `muscData` package. Below the code used to subset the original dataset.

### Author(s)

Simone Tiberi simone.tiberi@uzh.ch

### See Also

`distinct_test`

### Examples

    ####################
    # Object 'Kang_subset' is generated as follows:
    ####################
    # library(muscData)
    # sce = Kang18_8vs8()
    #
    # library(scater)
    # sce = computeLibraryFactors(sce)
    # sce = logNormCounts(sce)
    # cpm(sce) <- calculateCPM(sce)
    #
    # Select genes with at least 1000 non-zero cells:
    # sce = sce[ rowSums(assays(sce)$counts > 0) >= 1000, ]
    #
    # randomly select 100 of these genes:
    # set.seed(61217)
    # sel = sample( rownames(sce), size = 100)
    # sce = sce[ rownames(sce) %in% sel, ]
    #
    # select 3 individuals only:
    # ind_selected = levels(factor(colData(sce)$ind))[1:3]
    # sce = sce[, sce$ind %in% ind_selected]
    #
    # make a sample_id column:
    # colData(sce)$sample_id = factor(paste(colData(sce)$stim, colData(sce)$ind, sep = "_"))
    #
    # create an experiment_info object containing sample-group information:
    # experiment_info = unique(data.frame(sample_id = colData(sce)$sample_id,
    #                                     stim = colData(sce)$stim) )
    # metadata(sce)$experiment_info = data.frame(experiment_info, row.names = NULL)
    #
    # remove unnecessary information to reduce storage space:
    # sce$cluster = NULL;
    # sce$multiplets = NULL;
    # rowData(sce) = NULL;
    # colnames(sce) = NULL;
    # reducedDim(sce) = NULL
    # sce$ind = NULL
    # sce$sizeFactor = NULL
    # rm assays counts
    # assays(sce) = assays(sce)[2:3]
    #
    # Kang_subset = sce
    # save(Kang_subset, file = "Kang_subset.RData")

[Package distinct version 1.4.1 Index]