mxnorm (version 1.0.3)

mx_dataset: Generates mx_dataset

Description

Takes in data from data.frame of cell-level multiplexed data to create a mx_dataset S3 object.

Usage

mx_dataset(data, slide_id, image_id, marker_cols, metadata_cols = NULL)

Value

data.frame object in the mx_dataset format with attribute for input type

Arguments

data

multiplexed data to normalize. Data assumed to be a data.frame with cell-level data.

slide_id

String slide identifier of input data. This must be a column in the data data.frame.

image_id

String image identifier of input data. This must be a column in the data data.frame.

marker_cols

vector of column name(s) in data corresponding to marker values.

metadata_cols

other identifiers of the input data (default=NULL). This must be a vector of column name(s) in the data data.frame.

Examples

mx_data = mx_dataset(mxnorm::mx_sample, "slide_id", "image_id",
  c("marker1_vals","marker2_vals","marker3_vals"),
  c("metadata1_vals"))