Description Usage Arguments Value Examples
reconstructCMAP
: calculate and remove principal components from Connectivity map data. If CMAP data matrix have already been reconstructed using the same PCs and pert_types this function will read previously saved SVD output and reconstructed CMAP data matrix
svdCMAP
: calculate and remove principal components from Connectivity map data. If CMAP data matrix have already been reconstructed using the same PCs and pert_types this function will read previously saved SVD output and reconstructed CMAP data matrix
1 2 3 4 5 6 7 8 9 10 11 | reconstructCMAP(CMap_files, remove_PCs = "none", return_PCs = T,
return_CMAP = T, save_CMAP = F, pert_types = c("trt_sh.cgs",
"trt_oe", "trt_cp", "trt_lig", "trt_oe.mut", "trt_xpr", "trt_sh.css",
"ctl_vehicle.cns", "ctl_vector.cns", "ctl_untrt.cns"))
svdCMAP(CMap_files, return_PCs = T, is_touchstone = "all",
pert_types = c("trt_sh.cgs", "trt_oe", "trt_cp", "trt_lig",
"trt_oe.mut", "trt_xpr", "trt_sh.css", "ctl_vehicle.cns",
"ctl_vector.cns", "ctl_untrt.cns"), pert_itimes = c("all"),
cell_ids = c("all"), gene_names = c("all"), keep_one_oe = "all",
landmark_only = F, ...)
|
CMap_files |
a list of directories and urls produced by |
remove_PCs |
integer or character, indexes - which principal components to remove. "none" to keep all PCs |
return_PCs |
logical, return the output of svd decomposition |
return_CMAP |
logical, return Connectivity map data reconstructed using only specified PCs |
save_CMAP |
logical, save Connectivity map data reconstructed using only specified PCs. Returned |
pert_types |
a character vector of perturbation types, query for available perturbation types using |
is_touchstone |
logical, select only the perturbation data that is a part of the touchstone dataset (genes profiled across all 9 core cell lines)? Details: https://docs.google.com/document/d/1q2gciWRhVCAAnlvF2iRLuJ7whrGP6QjpsCMq1yWz7dU/ |
pert_itimes |
a character vector of perturbation times, query for available perturbation times using |
cell_ids |
a character vector of cell line names, query for available cell line names using |
gene_names |
a character vector of HUGO gene names. Use |
keep_one_oe |
keep only one overexpression experiment per gene and condition. Applicable only when |
landmark_only |
read only landmark genes (rows, measured). Details: https://docs.google.com/document/d/1q2gciWRhVCAAnlvF2iRLuJ7whrGP6QjpsCMq1yWz7dU/edit |
... |
passed to svd: |
CMap_files |
a list of directories and urls produced by |
return_PCs |
logical, return the output of svd decomposition. Alternatively just calculate and save. |
pert_types |
a character vector of perturbation types, query for available perturbation types using |
reconstructCMAP
:
svdCMAP
:
1 2 3 4 |
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