create_SE {barcodetrackR} | R Documentation

## create_SE

### Description

Creates a SummarizedExperiment object from a data frame containing clonal tracking counts ('your_data') with rows as observations and columns as samples, and the associated metadata ('meta_data') with rows as samples and columns of information describing those samples.

### Usage

    create_SE(
      your_data = NULL,
      meta_data = NULL,
      threshold = 0,
      threshold_type = "relative",
      log_base = exp(1),
      scale_factor = 1e+06
    )

### Arguments

`your_data` | A data frame. For clonal tracking data, this will be individual barcodes or lineage tracing elements in rows and samples in columns.
`meta_data` | A data frame containing all meta-data. Must, at the very least, include a column called "SAMPLENAME" that contains all of the colnames within the data frame passed as 'your_data' and only those colnames.
`threshold` | Numeric. The minimum threshold abundance for a barcode to be maintained in the SE. If 'threshold_type' is relative, this parameter should be between 0 and 1. If 'threshold_type' is absolute, this parameter should be greater than 1.
`threshold_type` | Character. One of "relative" or "absolute" relative. If a relative threshold is specified, only those rows which have higher than 'threshold' proportion of reads within at least one sample will be kept as non-zero. If an absolute threshold is specified, only those rows which have an absolute read count higher than 'threshold' in at least one sample will be kept as non-zero.
`log_base` | A numeric indicating which base to use when logging the normalized data
`scale_factor` | A numeric indicating what scaling factor to use in normalization. For the default value of 1 million, barcode proportions on a per sample basis will be multiplied by 1 million before log+1 normalization.

### Value

Returns a SummarizedExperiment holding your clonal tracking data and the associated metadata.

### Examples

    count_path <- system.file("extdata",
        "/WuC_etal_appdata/sample_data_ZJ31.txt",
        package = "barcodetrackR"
    )
    wu_dataframe <- read.delim(count_path, row.names = 1)
    metadata_path <- system.file("extdata",
        "/WuC_etal_appdata/sample_metadata_ZJ31.txt",
        package = "barcodetrackR"
    )
    wu_metadata <- read.delim(metadata_path)
    wu_SE <- create_SE(
        your_data = wu_dataframe, meta_data = wu_metadata,
        threshold = 0
    )

[Package barcodetrackR version 1.0.0 Index]