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functions.md

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ProjecTILs - Functions

  • load.reference.map Load or download the reference map for dataset projection. By the default it downloads the reference atlas of tumour-infiltrating lymphocytes (TILs).

  • read.sc.query Load a query expression matrix to be projected onto the reference atlas. Several formats (10x, hdf5, raw and log counts, etc.) are supported - see type parameter for details

  • make.projection Project a single-cell RNA-seq dataset onto a reference map of cellular states.

  • plot.projection Plots the UMAP representation of the reference map, together with the projected coordinates of a query dataset.

  • cellstate.predict Use a nearest-neighbor algorithm to predict a feature (e.g. the cell state) of the query cells.

  • plot.statepred.composition Makes a barplot of the frequency of cell states in a query object.

  • plot.states.radar Makes a radar plot of the expression level of a specified set of genes.

  • find.discriminant.dimensions Searches PCA or ICA dimensions where the query set deviates the most from a control set or from the reference map.

  • plot.discriminant.3d Add an extra dimension to the reference map to explore additional axes of variability in a query dataset compared to the reference map.

  • find.discriminant.genes Performs differential expression analysis between a projected query and a control (either the reference map or a control sample), for a selected reference subtype. Useful to detect whether specific cell states over/under-express genes between conditions or with respect to the reference.

Find more information, syntax and examples using the R help function e.g. ?make.projection