Description Usage Arguments Details See Also Examples
Functions for the palasso
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X |
covariates: matrix with n rows and p columns |
filter |
numeric, multiplying the sample size |
cutoff |
character "zero", "knee", or "half" |
scale |
logical |
x |
covariates: list of length k, including matrices with n rows and p columns |
effects |
number of causal covariates: vector of length k |
y |
response: vector of length n |
nfolds.ext |
number of external folds |
... |
arguments for palasso |
index |
indices of causal covariates: list of length k, including vectors |
trial |
development option |
.prepare
:
pre-processes sequencing data by
removing features with a low total abundance,
and adjusting for different library sizes;
obtains two transformations of the same data
by (1) binarising the counts with some cutoff
and (2) taking the Anscombe transform;
scales all covariates to mean zero and unit variance.
.simulate
:
simulates the response by
exploiting two experimental covariate matrices;
allows for different numbers of non-zero coefficients for X and Z.
.predict
:
estimates the predictive performance of different lasso models
(standard X and/or Z, adaptive X and/or Z, paired X and Z);
minimises the loss function "deviance", but also returns other loss functions;
supports logistic and Cox regression.
.select
:
estimates the selective performance of different lasso models
(standard X and/or Z, adaptive X and/or Z, paired X and Z);
limits the number of covariates to 10;
returns the number of selected covariates,
and the number of correctly selected covariates.
Use palasso to fit the paired lasso.
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