Cluster assignment for cells based on per cell gene expression profile and reference profiles in example data set

The example dataset is based on the cropped regions from two different FOVs of same SMI RNA readout run for FFPE melanoma tissue sample. The corresponding raw transcript data files are

• extdata/Run4104_FOV001__complete_code_cell_target_call_coord.csv

• extdata/Run4104_FOV002__complete_code_cell_target_call_coord.csv

Each raw transcript data files have 1 transcript per row with 25 different meta information in columns. Some important columns are

x

spatial coordinate of the transcript in x-axis of the given FOV, unit in pixel, 0.18um per pixel

y

spatial coordinate of the transcript in y-axis of the given FOV, unit in pixel, 0.18um per pixel

z

spatial coordinate of the transcript in z-axis of the given FOV, unit in z-step, 0.8um per z-step

target

gene identity of given transcript

CellId

the cell label assignment of given transcript within given FOV based on original cell segmentation

The cluster assignment for each cell is calculated based on the corresponding per cell gene expression profiles, data/example_CellGeneExpr.RData, and reference profiles, data/example_refProfiles.RData.

Usage

data(example_clust)

Format

An object of class "character" with 754 cells in same order as the cells in the row of data/example_CellGeneExpr.RData.

See also

example_CellGeneExpr for corresponding cell x gene expression matrix, example_refProfiles for the reference profiles used for cluster assignment