refit_w_comparison: Replicate cell type fraction analysis of Koestler et al. and...
In cozygene/CellTypeSpecificMethylationAnalysis: Evaluation of Cell Type Specific Methylation Analysis
Description
Usage
Arguments
Value
View source: R/refit_w_comparison.r
Description
Replicate cell type fraction analysis of Koestler et al. and BBC datasets
Usage
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refit_w_comparison(
bbc_pheno_path,
bbc_facs_path,
data_dir,
plot_dir,
plot_type = "tiff",
n.sites = NULL
)
Arguments
bbc_pheno_path
Path to PhenoTypesBBC.Rd (provided by Jing et al.) which contains
covariates for the BBC dataset
bbc_facs_path
Path to facsBBC.Rd (provided by Jing et al.) which contains
FACS-based cell fractions for the BBC dataset
data_dir
Directory to store BBC data
plot_dir
Directory to save plot of results
plot_type
Extension for saving plot graphics, such as pdf or png
n.sites
Number of sites to subset for quick testing purposes.
Value
A list of results. Slot results contains a list of proportions and metrics generated
by each method on each dataset. Slot plot contains the plot object
cozygene/CellTypeSpecificMethylationAnalysis documentation built on Jan. 28, 2022, 11:20 a.m.
R Package Documentation
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Description Usage Arguments Value
View source: R/refit_w_comparison.r
Description
Replicate cell type fraction analysis of Koestler et al. and BBC datasets
Usage
1 2 3 4 5 6 7 8 | refit_w_comparison(
bbc_pheno_path,
bbc_facs_path,
data_dir,
plot_dir,
plot_type = "tiff",
n.sites = NULL
)
|
Arguments
bbc_pheno_path |
Path to PhenoTypesBBC.Rd (provided by Jing et al.) which contains covariates for the BBC dataset |
bbc_facs_path |
Path to facsBBC.Rd (provided by Jing et al.) which contains FACS-based cell fractions for the BBC dataset |
data_dir |
Directory to store BBC data |
plot_dir |
Directory to save plot of results |
plot_type |
Extension for saving plot graphics, such as pdf or png |
n.sites |
Number of sites to subset for quick testing purposes. |
Value
A list of results. Slot results contains a list of proportions and metrics generated
by each method on each dataset. Slot plot contains the plot object
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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