News about the tcgsaseq
R package
Main changes in Version 1.8.1 (2018-12-06):
- perm_pe function for exact p-values and accurate FDR control when using permutation test. The column names of the
$pvals
output are back to being the same regardless of the test chosen being asympotic
or permutation
- dsFDR is not used anymore
Main changes in Version 1.8.0 (2018-11-23):
- dsFDR function for accurate discrete FDR control when using permutation test. This changes the column names of the
$pvals
output when which_test = permutations
Main changes in Version 1.7.2 (2018-07-18):
Main changes in Version 1.7.1 (2018-07-07):
Main changes in Version 1.6.5 (2017-12-24) — this is only a minor release:
- bug fix in the log2-cpm transformation computation (for
preprocessed = FALSE
) in sp_weights
- bug fix in
sp_weights
when facing NA
or NaN
values
Main changes in Version 1.6.3 (2017-11-09)
WARNING
instead of ERROR
when a gene set with no measured genes is tested
NA
support through na.rm_...
logical arguments
- bug fix for row.names error in weights computation for gene-wise analysis
Main changes in Version 1.6.2 (2017-08-04)
- bug fix to the log2-cpm transformation computation (for
preprocessed = FALSE
)
- improvement to defaults in
varseq
and tcgsa_seq
wrapper functions, including an option to compute heteroscedasticity weights without conditioning on the variable(s) to be tested
Main changes in Version 1.5.2 (2017-07-11)
- user-friendly wrapper function
varseq
for gene-wise testing
- RAM usage optimization
Main changes in Version 1.5.1 (2017-05-24) — this is only a minor release:
- homogeneous test now available for gene-wise testing.
Main changes in Version 1.5.0 (2017-03-27):
- permutation test now available for gene-wise testing
Main changes in Version 1.4.0 (2017-02-21):
- bug fix for gene-wise testing
Main changes in Version 1.3.1 (2016-11-24):
- bug fix for testing several covariates together (such as several bases of time) which now gives correct p-values
- support for gene-wise testing
- example dataset ‘baduel_small’ was changed to ‘baduel_5gs’ which includes 1943 additional gene expressions and the definition of 5 gene sets
- documentation updated
Main changes in Version 1.2.0 (2016-07-19):
- support homogeneous gene set test
- documentation updated
Main changes in Version 1.1.0 (2016-05-26):
- improved imports
- documentation updated
Main changes in Version 1.0.2 (2016-05-18) — this is only a minor release:
- documentation and CITATION updated
Main changes in Version 1.0.1 (2016-05-14) — this is only a minor release: