findSignatures {deconvR} | R Documentation

## A function to construct a signature matrix

### Description

A function to construct a signature matrix

### Usage

    findSignatures(samples, sampleMeta, atlas = NULL, variation_cutoff = NULL)

### Arguments

`samples` | dataframe, has first column IDs, rest of columns are samples (must have column name as sample accession ID which should be found in sampleMeta), rows are units of signature (e.g. CpGs)
`sampleMeta` | dataframe, must have first column for accession ID of each sample, and second column for cell type of sample, rows are samples
`atlas` | dataframe, the reference atlas to which new signatures can be added, if not present then a new reference atlas will be created using sample(s). Should be dataframe with column for each cell type, rows units of signature (e.g. CpGs)
`variation_cutoff` | either a number between 0 to 1, or NULL.For multiple samples from the same cell type, ignore CpGs with variation > variation_cutoff with that cell type. defaults to NULL (i.e. no cutoff)

### Value

A dataframe extendedAtlas which contains all cell types in atlas (if given), and those in samples added by cell type, has first column "IDs", rest of columns are cell types, rows are have first cell with the ID (e.g. CpG ID) and then values of signature (e.g. methylation values)

### Examples

    data("HumanCellTypeMethAtlas")
    exampleSamples <- simulateCellMix(1,
        reference = HumanCellTypeMethAtlas
    )$simulated
    exampleMeta <- data.table(
        "Experiment_accession" = "example_sample",
        "Biosample_term_name" = "example_cell_type"
    )
    colnames(exampleSamples)[-1] <- c("example_sample")
    signatures <- findSignatures(
        samples = exampleSamples,
        sampleMeta = exampleMeta
    )
    signatures <- findSignatures(
        samples = exampleSamples, sampleMeta = exampleMeta,
        atlas = HumanCellTypeMethAtlas
    )

[Package deconvR version 1.0.1 Index]