create_SE: create_SE

In dunbarlabNIH/barcodetrackR: Functions for Analyzing Cellular Barcoding Data

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
)

dunbarlabNIH/barcodetrackR documentation built on April 26, 2021, 6:20 p.m.