SingleR-class: An S4 class to represent SingleR objects This object can be...

In dviraran/SingleR: Reference-based single-cell RNA-seq annotation

Description

An S4 class to represent SingleR objects This object can be upload to the SingleR browser (http)

Slots

project.name

a string. Must be the same as the file name.

xy

matrix of the xy coordinates. Row names must be single-cell names.

labels

data.frame of the SingleR annotations. Rows are single-cell, a column for each annotation by reference. Column names are the reference name (e.g. Immgen, Immgen.main, Blueprint+Encode, etc.)

labels.NFT

Same as labels. Annotation before fine-tuning.

labels.clusters

data.frame. Same as labels, but a row for each cluster, not single-cell.

labels.clusters.NFT

Same as labels.clusters. Annotation before fine-tuning.

clusters

data.frame. Rows are single-cell, columns are clusters. Multiple clsutering are possible.

ident

data.frame. Rows are single-cell, columns are caterogical meta.data (e.g. orig.ident).

other

data.frame. Rows are single-cell, columns are continous variables (e.g. cell cycle score).

scores

list. Each item in the list corresponds to the column labels in labels. Items are the SingleR score matrices.

meta.data

character array. Each item is a named charachter (e.g. Citation, Organism, Technology)

expr

a matrix. The single-cell expression matrix.

dviraran/SingleR documentation built on April 21, 2020, 3:23 p.m.