cocoreg: Extracts Shared Variation in Collections of Datasets Using Regression Models

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The cocoreg algorithm extracts shared variation from a collection of datasets using regression models.

Author
Jussi Korpela [aut, cre], Andreas Henelius [aut], Finnish Institute of Occupational Health [cph]
Date of publication
2016-05-03 18:35:21
Maintainer
Jussi Korpela <jussi.korpela@iki.fi>
License
MIT + file LICENSE
Version
0.1.0

View on CRAN

Man pages

add_notches
Add notch-like gaussian snippets to an existing signal x
apply_dc_meta
Apply extracted properties of a data collection to a data...
average_R2_dflst
Computes the R^2 (variance explained) between two lists of...
BGFA_cocoreg_interface
Apply GFA using the same interface as cocoreg()
BGFA_joint_info
Project BGFA components common to all datasets back to the...
cocoreg
The Common Components by Regression (CoCoReg) algorith.
cocoreg_by_path
Compute D_joint for dataset i separately for all paths Can be...
compose
Calculate the composition formed by applying all functions in...
compose_all
Calculate the average of the composition formed by applying...
create_mappings
Generate all possible pairwise mappings between the given...
create_syndata_mv
Create multivariate synthetic data
create_syn_data_puvar
A data collection with variables that "become unrelated...
create_syndata_pwl
A non-linear data collection using piecewise linearity
create_syn_data_toy
An illustrative synthetic datacollection
create_syn_data_uds
A data collection with one unrelated dataset
create_syn_data_uvar
A dollection with unrelated variables
create_Z_linear
Contains functions to create synthetic datasets with...
cshift
Circularly shift vector elements
data_collections2ggdf
Catenate a set of data collections (lists of data.frames)...
data_matrix_rmse
Compute RMSE between data.matrices dm1 and dm2
dc_variability
Compute ds_variability for all datasets in a data collection
df_ggplot_melt
Melt data.frame into ggplottable format
dflst2array
Catenate a list of data.frames to a matrix along dim
dflst2df
Catenate a list of data.frames vertically to a single...
dflst2dfmelt
Combine a list of data.frames to a single molten data.frame
dflst_add_ds
Add a data.frame (dataset) to a list of data.frames...
dflst_dsnames2varnames
Append dataset names to variable names of the respective...
dflst_pca
Apply PCA to the data after catenating data.frames...
df_scale
Apply scale on a numeric data.frame
df_scale_ols
Scales variables in data.frame dfx using ordinary least...
dl_remove_NA
Remove rows with NA values from a list of data.frames
dl_scale
Run scale() on a list of data.frames
ds_variability
Compute variability_components for a dataset
generate_mapping_function
Generate a mapping function between two datasets
generate_paths
Generate all/some paths between points
generate_paths_cyclic
Generate cyclic paths
generate_paths_noncyclic
Generate non-cyclic paths
get_dc_meta
Extract important properties of data collection
get_range_datalist
Get [min, max] of a list of numeric objects
get_starting_dataset
Helper function to get the starting dataset based on a path.
ggcompare_dclst
Compare data collections variable by variable
ggplot_dclst
Plotting data collections using ggplot
ggplot_df
Plotting data.frame using ggplot
ggplot_dflst
Plot a list of data.frames using ggplot2
make_data_gauss_2d
Make 2D gauss data (maybe obsolete)
mapping_glmnet
Define a mapping function using glmnet::glmnet
mapping_lm
Mapping stats::lm
mapping_lmridge
Define a mapping function using MASS::lm.ridge
mapping_pcr
Define a mapping function using pls::pcr
mapping_rf
Mapping randomForest
mapping_rlm
Mapping MASS::rlm
mappings_R2_matrix
Extract R2 values from a list of mappings using summary()
mapping_svm
Mapping svm
mapping_svm_sigmoid
Mapping svm using sigmoid
matrix_variability
Compute "variance" of the matrices using Frobenius norm....
nplst_reorder_grid
Reorders a nested list of ggplots
pathify
Create a path
PCA_cocoreg_interface
PCA projection using cocoreg interface
rename_variables
Rename variables of a data collection
repmat
Replicate matrix to create a larger one
RGCCA_cocoreg_interface
COCOREG style analysis using RGCCA projection
rmse
Compute RMSE between vectors v1 and v2
rotation_matrix
A rotation matrix
row_suffle_variability
Determine the variability of matrices under row suffling
SCA_cocoreg_interface
SCA projection using cocoreg interface
se
Standard error of mean
ss
Sum of squares
svm_sigmoid
SVM using sigmoid kernel
to_unit_vec
Make vector of unit norm
traverse_nested_list
Apply fun to the bottom level of a nested list structure
validate_data
Validate a data collection for use with cocoreg
var_explained
Sum-of-squares values showing what portion of variance in...
variability_components
Compute total, within group and between group variability...
variation_shared_by
Return a specific variation component
vecnorm
Compute Euclidean norm of vector
vector_variability
Compute "variance" of the vectors var()
wrapper_BGFA
Run BGFA by Klami et al using data format conventions of this...

Files in this package

cocoreg
cocoreg/inst
cocoreg/inst/doc
cocoreg/inst/doc/cocoreg-basics.html
cocoreg/inst/doc/cocoreg-basics.R
cocoreg/inst/doc/cocoreg-basics.Rmd
cocoreg/NAMESPACE
cocoreg/R
cocoreg/R/common_tools.R
cocoreg/R/cocoreg.R
cocoreg/R/common_plots.R
cocoreg/R/synthetic_datasets.R
cocoreg/vignettes
cocoreg/vignettes/cocoreg-basics.Rmd
cocoreg/README.md
cocoreg/MD5
cocoreg/build
cocoreg/build/vignette.rds
cocoreg/DESCRIPTION
cocoreg/man
cocoreg/man/mapping_rf.Rd
cocoreg/man/apply_dc_meta.Rd
cocoreg/man/BGFA_cocoreg_interface.Rd
cocoreg/man/generate_paths_cyclic.Rd
cocoreg/man/compose.Rd
cocoreg/man/mapping_rlm.Rd
cocoreg/man/cocoreg.Rd
cocoreg/man/ggplot_dclst.Rd
cocoreg/man/make_data_gauss_2d.Rd
cocoreg/man/rmse.Rd
cocoreg/man/compose_all.Rd
cocoreg/man/variability_components.Rd
cocoreg/man/repmat.Rd
cocoreg/man/create_syn_data_toy.Rd
cocoreg/man/traverse_nested_list.Rd
cocoreg/man/mapping_pcr.Rd
cocoreg/man/dl_scale.Rd
cocoreg/man/mapping_lmridge.Rd
cocoreg/man/ss.Rd
cocoreg/man/vecnorm.Rd
cocoreg/man/get_dc_meta.Rd
cocoreg/man/dflst2array.Rd
cocoreg/man/to_unit_vec.Rd
cocoreg/man/create_syn_data_uds.Rd
cocoreg/man/dflst2df.Rd
cocoreg/man/dc_variability.Rd
cocoreg/man/dflst_add_ds.Rd
cocoreg/man/df_scale.Rd
cocoreg/man/add_notches.Rd
cocoreg/man/create_syndata_pwl.Rd
cocoreg/man/ggplot_dflst.Rd
cocoreg/man/SCA_cocoreg_interface.Rd
cocoreg/man/create_syn_data_uvar.Rd
cocoreg/man/ds_variability.Rd
cocoreg/man/generate_mapping_function.Rd
cocoreg/man/df_scale_ols.Rd
cocoreg/man/get_range_datalist.Rd
cocoreg/man/variation_shared_by.Rd
cocoreg/man/get_starting_dataset.Rd
cocoreg/man/mappings_R2_matrix.Rd
cocoreg/man/pathify.Rd
cocoreg/man/average_R2_dflst.Rd
cocoreg/man/vector_variability.Rd
cocoreg/man/validate_data.Rd
cocoreg/man/RGCCA_cocoreg_interface.Rd
cocoreg/man/mapping_glmnet.Rd
cocoreg/man/se.Rd
cocoreg/man/row_suffle_variability.Rd
cocoreg/man/dflst2dfmelt.Rd
cocoreg/man/cshift.Rd
cocoreg/man/generate_paths.Rd
cocoreg/man/PCA_cocoreg_interface.Rd
cocoreg/man/mapping_svm.Rd
cocoreg/man/wrapper_BGFA.Rd
cocoreg/man/rotation_matrix.Rd
cocoreg/man/dl_remove_NA.Rd
cocoreg/man/df_ggplot_melt.Rd
cocoreg/man/generate_paths_noncyclic.Rd
cocoreg/man/ggplot_df.Rd
cocoreg/man/nplst_reorder_grid.Rd
cocoreg/man/mapping_svm_sigmoid.Rd
cocoreg/man/rename_variables.Rd
cocoreg/man/data_collections2ggdf.Rd
cocoreg/man/dflst_dsnames2varnames.Rd
cocoreg/man/dflst_pca.Rd
cocoreg/man/matrix_variability.Rd
cocoreg/man/create_syn_data_puvar.Rd
cocoreg/man/create_mappings.Rd
cocoreg/man/ggcompare_dclst.Rd
cocoreg/man/create_Z_linear.Rd
cocoreg/man/svm_sigmoid.Rd
cocoreg/man/create_syndata_mv.Rd
cocoreg/man/BGFA_joint_info.Rd
cocoreg/man/cocoreg_by_path.Rd
cocoreg/man/var_explained.Rd
cocoreg/man/data_matrix_rmse.Rd
cocoreg/man/mapping_lm.Rd
cocoreg/LICENSE