docs/functions.md

In carmonalab/ProjecTILs: Reference-based analysis of scRNA-seq data

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

• Run.ProjecTILs A wrapper for make.projection and cellstate.predict (see below). It returns the query embedded in the PCA and UMAP space of the reference, and predict cell state labels for the query cells.

• ProjecTILs.classifier Similarly to Run.ProjecTILs, it perform reference projection and cell state prediction. However, the query embeddings are left intact and only cell state labels are returned. Useful if you wish to use ProjecTILs as a classifier and annotate your data in their native space.

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

• celltype.heatmap Generate a averaged gene expression heatmap from a Seurat object

• 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.

• make.reference Converts a Seurat object into a custom reference map for ProjecTILs.

• recalculate.embeddings After projection of query data into a reference, you may want to recalculate the low-dimensional embeddings accounting for the new data. The resulting object can be used as a new reference.

• merge.Seurat.embeddings Given two Seurat objects, merge counts and data as well as dim reductions (PCA, UMAP, ICA, etc.)

• compute_silhouette Given a projected object and its reference, calculate silhouette coefficient for query cells with respect to reference cells with the same cell labels.

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

carmonalab/ProjecTILs documentation built on April 13, 2025, 10:04 p.m.