read.SpatialRNA: Creates a SpatialRNA object from a coords and counts file
In dmcable/RCTD: SpatialeXpressionR: Cell type identification and cell type-specific differential expression in spatial transcriptomics
read.SpatialRNA R Documentation
Creates a SpatialRNA object from a coords and counts file
Description
Warning: this function is provided out of convenience for experienced users, but
we can not provide direct support for debugging file input errors. If you are obtaining
errors from this method, we recommend a less error-prone procedure of loading in your
coords and counts matrices in first and then using the 'SpatialRNA' constructor function,
which will systematically check for errors in the inputs.
Usage
read.SpatialRNA(datadir, count_file = "counts.csv", coords_file = "coords.csv")
Arguments
datadir
(character) full path to input directory
count_file
(character) file name of the counts csv file (genes by pixels matrix)
coord_file
(character) file name of the coords csv file (pixels by (barcodes, x, y) matrix)
Details
The coords matrix needs to be formated as columns (barcodes, x, y)
Value
Returns a SpatialRNA object containing the coordinates and counts
from the input files
dmcable/RCTD documentation built on Feb. 24, 2024, 11:03 p.m.
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| read.SpatialRNA | R Documentation |
Creates a SpatialRNA object from a coords and counts file
Description
Warning: this function is provided out of convenience for experienced users, but we can not provide direct support for debugging file input errors. If you are obtaining errors from this method, we recommend a less error-prone procedure of loading in your coords and counts matrices in first and then using the 'SpatialRNA' constructor function, which will systematically check for errors in the inputs.
Usage
read.SpatialRNA(datadir, count_file = "counts.csv", coords_file = "coords.csv")
Arguments
datadir |
(character) full path to input directory |
count_file |
(character) file name of the counts csv file (genes by pixels matrix) |
coord_file |
(character) file name of the coords csv file (pixels by (barcodes, x, y) matrix) |
Details
The coords matrix needs to be formated as columns (barcodes, x, y)
Value
Returns a SpatialRNA object containing the coordinates and counts
from the input files
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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