loadFry {fishpond} | R Documentation |
Enables easy loading of sparse data matrices provided by alevin-fry USA mode. Alevin-fry - https://www.biorxiv.org/content/10.1101/2021.06.29.450377v1
load_fry_raw(fryDir, quiet = FALSE) loadFry(fryDir, outputFormat = "scRNA", nonzero = FALSE, quiet = FALSE)
fryDir |
path to the output directory returned by
alevin-fry quant command. This directory should contain a
|
quiet |
logical whether to display no messages |
outputFormat |
can be either be a list that defines the
desired format of the output |
nonzero |
whether to filter cells with non-zero expression
value across all genes (default |
A SingleCellExperiment
object that contains one
or more assays. Each assay consists of a gene by cell count matrix.
The row names are feature names, and the column names are cell
barcodes
loadFry
This function consumes the result folder returned by running
alevin-fry quant in unspliced, spliced, ambiguous (USA)
quantification mode, and returns a SingleCellExperiement
object
that contains a final count for each gene within each cell. In
USA mode, alevin-fry quant returns a count matrix contains three
types of count for each feature (gene) within each sample (cell
or nucleus), which represent the spliced mRNA count of the gene (S),
the unspliced mRNA count of the gene (U), and the count of UMIs whose
splicing status is ambiguous for the gene (A). For each assay
defined by outputFormat
, these three counts of a gene
within a cell will be summed to get the final count of the gene
according to the rule defined in the outputFormat
. The
returned object will contains the desired assays defined by
outputFormat
, with rownames as the barcode of samples and
colnames as the feature names.
The outputFormat
argument takes either be a list that defines
the desired format of the output
SingleCellExperiment
object or a string that represents one of
the pre-defined output format.
Currently the pre-defined formats
of the output SingleCellExperiment
object are:
This format is recommended for single cell experiments.
It returns a counts
assay that contains the S+A count of each gene in each cell.
This format is recommended for single nucleus experiments.
It returns a counts
assay that contains the U+S+A count of each gene in each cell.
This format put the three kinds of counts into three separate assays,
which are unspliced
, spliced
and ambiguous
.
This format contains two assays.
The spliced
assay contains the S+A count of each gene in each cell.
The unspliced
assay contains the U counts of each gene in each cell.
This format is for direct entry into velociraptor R package or other scVelo downstream analysis pipeline for velocity analysis in R with Bioconductor. It adds the expected "S"-pliced assay and removes errors for size factors being non-positive.
A custom output format can be defined using a list. Each element in the list
defines an assay in the output SingleCellExperiment
object.
The name of an element in the list will be the name of the corresponding
assay in the output object. Each element in the list should be defined as
a vector that takes at least one of the three kinds of count, which are U, S and A.
See the provided toy example for defining a custom output format.
load_fry_raw
This function processes alevin-fry's quantification result
contained within the input folder.This function returns a list
that consists of the gene count matrix, the gene names list, the
barcode list, and some metadata, such as the number of genes in
the experiment and whether alevin-fry was executed in USA
mode. In the returned list, the all-in-one count matrix,
count_mat
, returned from the USA mode of alevin-fry
consists of the spliced count of genes defined in
gene.names
for all barcodes defined in barcodes
,
followed by the unspliced count of genes in the same order for
all cells, then followed by the ambiguous count of genes in the
same order for all cells.
# Get path for minimal example avelin-fry output dir testdat <- fishpond:::readExampleFryData("fry-usa-basic") # This is exactly how the velocity format defined internally. custom_velocity_format <- list("spliced"=c("S","A"), "unspliced"=c("U")) # Load alevin-fry gene quantification in velocity format sce <- loadFry(fryDir=testdat$parent_dir, outputFormat=custom_velocity_format) SummarizedExperiment::assayNames(sce) # Load the same data but use pre-defined, velociraptor R pckage desired format scvelo_format <- "scVelo" scev <- loadFry(fryDir=testdat$parent_dir, outputFormat=scvelo_format, nonzero=TRUE) SummarizedExperiment::assayNames(scev)