import_velo_txis: import velocity information (usually from Alevin) into a...
In trichelab/velocessor: The world's dumbest single-cell RNA velocity calculator and loader
Description
Usage
Arguments
Details
Value
View source: R/import_velo_txis.R
Description
This function is usually called by process_velo_txis(). The 'cdat' argument
takes a single-row data.frame containing 'names' and 'files' as its columns.
'quant' is the type of quantifications; at present, only alevin is supported.
'sep' allows deduplicating barcodes by sample using cbind without incident
once the results of import_velo_txis are returned to process_velo_txis.
Usage
1
import_velo_txis(cdat, quant = c("alevin"), meta = FALSE, QC = TRUE, sep = "_")
Arguments
cdat
A row of the colData prepared by process_velo_txis.
quant
What type of quantifications are these? ("alevin")
meta
Use tximeta for imports? (FALSE; can fail unexpectedly)
QC
Perform rudimentary quality control? (TRUE)
sep
What string separates sample name from barcode? ("_")
Details
FIXME: Add Kallisto support and Arkas style txome/repeatome/spikeome support.
Value
1
A SingleCellExperiment with 'spliced' & 'unspliced' assays.
trichelab/velocessor documentation built on Jan. 5, 2022, 6:27 p.m.
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Description Usage Arguments Details Value
View source: R/import_velo_txis.R
Description
This function is usually called by process_velo_txis(). The 'cdat' argument takes a single-row data.frame containing 'names' and 'files' as its columns. 'quant' is the type of quantifications; at present, only alevin is supported. 'sep' allows deduplicating barcodes by sample using cbind without incident once the results of import_velo_txis are returned to process_velo_txis.
Usage
1 | import_velo_txis(cdat, quant = c("alevin"), meta = FALSE, QC = TRUE, sep = "_")
|
Arguments
cdat |
A row of the colData prepared by process_velo_txis. |
quant |
What type of quantifications are these? ("alevin") |
meta |
Use tximeta for imports? (FALSE; can fail unexpectedly) |
QC |
Perform rudimentary quality control? (TRUE) |
sep |
What string separates sample name from barcode? ("_") |
Details
FIXME: Add Kallisto support and Arkas style txome/repeatome/spikeome support.
Value
1 | A SingleCellExperiment with 'spliced' & 'unspliced' assays.
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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