cal_all_tools: calculation seven tools
In zgyaru/testSctpa: A portable toolkit for pathway activity score calculation
Usage
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cal_all_tools(
seurat_object,
gSets_path,
tools = c("AUCell", "Vision", "GSVA", "ssGSEA", "plage", "zscore"),
normalize = c("log", "CLR", "RC", "scran", "none"),
mat_type = "counts",
n_cores = 3,
rand_seed = 123
)
Arguments
gSets_path
patwhays/gene sets in clasical GMT format
normalize
normalization method
counts
gene expresion matrix, rows are genes and cols are cells
tool
select PAS tools
filter
whether filtering for genes expressed in less than 5
parameters 'counts', 'gSets_path' and 'gSets' are consistent across all tools
other parameters see details of tools
zgyaru/testSctpa documentation built on Dec. 23, 2021, 9:17 p.m.
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Usage
1 2 3 4 5 6 7 8 9 | cal_all_tools(
seurat_object,
gSets_path,
tools = c("AUCell", "Vision", "GSVA", "ssGSEA", "plage", "zscore"),
normalize = c("log", "CLR", "RC", "scran", "none"),
mat_type = "counts",
n_cores = 3,
rand_seed = 123
)
|
Arguments
gSets_path |
patwhays/gene sets in clasical GMT format |
normalize |
normalization method |
counts |
gene expresion matrix, rows are genes and cols are cells |
tool |
select PAS tools |
filter |
whether filtering for genes expressed in less than 5 |
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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