cal_all_tools: calculation seven tools
In ZhangBuDiu/PASBench: benchmarking study of seven (PAS) tools for scRNA-seq analysis
Usage
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cal_all_tools(
counts,
gSets_path,
tools = c("AUCell", "pagoda2", "fscLVM", "Vision", "ROMA", "GSVA", "ssGSEA", "plage",
"zscore"),
filter = F,
normalize = c("log", "CLR", "RC", "scran", "sctransform", "none"),
n_cores = 3,
rand_seed = 123
)
Arguments
counts
gene expresion matrix, rows are genes and cols are cells
gSets_path
patwhays/gene sets in clasical GMT format
filter
whether filtering for genes expressed in less than 5
\itemnormalizenormalization method
\itemtoolselect PAS tools
parameters 'counts', 'gSets_path' and 'gSets' are consistent across all tools
other parameters see details of tools
ZhangBuDiu/PASBench documentation built on Sept. 26, 2021, 1:30 a.m.
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Usage
1 2 3 4 5 6 7 8 9 10 | cal_all_tools(
counts,
gSets_path,
tools = c("AUCell", "pagoda2", "fscLVM", "Vision", "ROMA", "GSVA", "ssGSEA", "plage",
"zscore"),
filter = F,
normalize = c("log", "CLR", "RC", "scran", "sctransform", "none"),
n_cores = 3,
rand_seed = 123
)
|
Arguments
counts |
gene expresion matrix, rows are genes and cols are cells |
gSets_path |
patwhays/gene sets in clasical GMT format |
filter |
whether filtering for genes expressed in less than 5 \itemnormalizenormalization method \itemtoolselect PAS tools |
parameters 'counts', 'gSets_path' and 'gSets' are consistent across all tools other parameters see details of tools
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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