Changes in version 1.11.1
- Fix bug on hlaToVariable() function that variable would erroneously
be named NA.
Changes in version 1.5.2
- alleles and KIR frequenceis updated.
- failed test fixed after update in tide dependence.
Changes in version 1.1.0
- Bioconductor release!
Changes in version 1.0.13
- adds new HLA-KIR interaction A03_A11_KIR3DL2 defined as (A03 | A11)
& KIR3DL2.
Changes in version 1.0.12
- fixes bug causing MiDAS subsetting to break omnibus testing.
Changes in version 1.0.11
- runMiDAS inheritance_model argument is no longer by defaut
'additive'. Now it is required to specify desired inheritance model,
when appplicable.
Changes in version 1.0.10
- fix bug causing Bw6 groups to be counted twice in hla_NK_lingads
experiment.
Changes in version 1.0.9
- fix bug causing runMiDAS errors when statistical model evaluated
with a warrning.
Changes in version 1.0.8
- fixed bug causing filterByVariables and filterByFrequency to strip
omnibus groups from target experiment.
Changes in version 1.0.7
- fixed bug causing HWETest filtration to strip omnibus groups from
target experiment
Changes in version 1.0.6
- removed unused expression dictionaries
Changes in version 1.0.4
- In frequency calculations the "NA"s were counted as non-carriers,
this has been changed such that "NA" samples are now omitted.
Changes in version 1.0.3
- warnings and errors occuring upon model evaluation are now
summarized into more readable form
Changes in version 1.0.2
- fixed problem vignettes index entry values, preventing vignettes
from being build
Changes in version 1.0.1
- fixed bug in summariseAAPos, where argument specifying AA position
didn't consider AA position numbering starting from negative
positions
- frequencies in getFrequencies output are no longer formatted as
percentages
- kableResults scroll box height can now be adjusted
- omnibus result columns: dof, residue were renamed to df, residues
- missing Bw6 references were added to allele_HLA_Bw dictionary
- new inheritance model has been added the overdominance
Changes in version 1.0.0
- reference frequencies for KIR genes has been added
- n_correction argument to runMiDAS has been modified such that for
Bonferroni correction it is possible to specify n_correction lower
than number of comparisons
- added option to specify amino acid selection used for Grantham
distance calculations
- custom HLA and KIR experiments has been added to prepareMiDAS
function
- kableResults function has been fixed
- HLA heterozygosity experiment has been added
Changes in version 0.99.33
- fixed bug causing hlaToAAVariation infer 2-digit alleles amino acid
sequences. Now 2-digit alleles are treated as NA.
Changes in version 0.99.31
- removed unneeded dependencies from package tutorial
- in the tutorial, external packages are now called explicitly
Changes in version 0.99.15
- fixes bug causing LRT to report wrong number of tested residues.
Changes in version 0.99.13
- changes version number to comply with Bioconductor package
submission guidelines.
- rename package to midasHLA; midas is already in use.
Changes in version 0.0.9048
- HWE test has been implemented
- midasToWide function has been optimized lowering significantly run
times
- Inheritance model specification has been moved from prepareMiDAS to
runMiDAS, improving logic of operations.
- added filtration by variables MiDAS method
- Frequency calcualtions can be now extended by the addition of
reference population frequencies
Changes in version 0.0.9047
- MiDAS object introduced
- This an object derived from MultiAssayExperiment class, it is used
for storing hla and kir calls and thier transformations. MiDAS
object is now returned by prepareMiDAS function. Functions like
getFrequencies work with MiDAS object, it can also be consumed as
data argument to functions such as lm.
- Updates the KIR output to the latest version, as well as updates
readKirCalls
- Implements omnibus and conditional omnibus tests that can be used
with "hla_aa" experiment
- Now argument analysis_type is changed to experiment
- experiments has been renamed eg. "aa_level" --> "hla_aa"
Changes in version 0.0.9046
- fixes bug causing prepareMiDAS to fail on 1 row hla_calls input for
'aa_level' analysis_type
Changes in version 0.0.9045
- fix bug treating NA values as distinct amino acid, that was adding
false columns to amino acids counts
Changes in version 0.0.9044
- changes amino acids numbering scheme to addhere with EBI convention
where numbering starts from -30 position
Changes in version 0.0.9043
- fixes hlaToAAVariation failing on mixed resolution hla_calls input
- adds warning when allele can not be found in the reference alignment
Changes in version 0.0.9042
- removes unused pvalue_cutoff argument from runMiDAS function
- fixes bug with conditional testing of glm models
Changes in version 0.0.9041
- fixes problem with placeholder (dummy variable) being constant. This
caused coxme function to throw errors upon model definition.
Changes in version 0.0.9040
- add functionality for Grantham distance calcualtion between amino
acid sequences (distGrantham function) and between HLA alleles
(hlaCallsGranthamDistance).
- add Grantham distances calculation for Class I HLA alleles to
prepareMiDAS and runMiDAS functionality.
Changes in version 0.0.9039
- now using interactions terms is possible through placeholder
argument in runMiDAS and presence of dummy var in input data frame
Changes in version 0.0.0.9038
- now variables passed to runMiDAS via variables argument are not
taken into account when applying frequency cut-off
Changes in version 0.0.0.9037
- adds new analysis type "none" to runMiDAS function. In this mode
only terms passed by variables argument are used.
Changes in version 0.0.0.9036
- refactor function for kabling results now it is much more general
and easier to use.
Changes in version 0.0.0.9035
- reading alignment files shipped with package is now faster.
- alignment files shipped with the packge are now stored in a
preparsed format.
- readHlaAlignments now have divergent behaviour if file is supplied
it behaves as previously, when gene is supplied it loads preparsed
alignment ommiting some lengthly steps. This change speeds up the
process but has no visible consequences.
- hlaToAAVariation no longer have alnpath argument. The variable amino
acid positions search in a custom alignment file can now be done
only manualy.
Changes in version 0.0.0.9034
- add function for models comparison using likelihood ratio test
(LRTest)
- add function for performing omnibus test on amino acid positions
(aaPosOmnibusTest)
- in summariseAAPosition output alleles numbers are now sorted
alphabeticaly
Changes in version 0.0.0.9033
- imporves documentation
- renames prepareMiDASData to prepareMiDAS
- renames analyzeMiDASData to runMiDAS
Changes in version 0.0.0.9032
- add function that lists HLA alleles and amino acid residues at a
given position together with frequencies.
Changes in version 0.0.0.9031
- add pattern argument to analyzeMiDASData that can be used to subset
variables choosen by analysis_type
Changes in version 0.0.0.9030
- add assert to test if there is appropiate tidy function available
Changes in version 0.0.0.9029
- fixes potential bug where NA is accepted as logical values in
is.flag asserts
Changes in version 0.0.0.9028
- fixes bug that was occuring when hla_calls passed to hlaToVariable
contained NAs every where except one column.
Changes in version 0.0.0.9027
- automated kabling of results from analyzeMiDASData function has been
removed, this can be now done by separate call to formatResults
function.
Changes in version 0.0.0.9026
- changes dictionaties naming convention. Now alleles dictionaties are
named Match_allele_HLA_name.txt
- add new functionality for converting counts to variables, new
dictionaries are named Match_counts_name.txt
Changes in version 0.0.0.9025
- changes the behavior of hlaToVariable and hlaCallsToCounts.
hlaToVariable now labels alleles not present in the dictionary
with 0, this can be changed with na.value argument. The NAs that
were already present in input hla_calls are preserved.
hlaCallsToCounts ignores all values that can be converted to numeric
- this way alleles that were not present in dictionary and are
represented as 0 are not counted.
Changes in version 0.0.0.9024
- adds n_correction argument to analyzeAssociations,
analyzeConditionalAssociations and analyzeMiDAS that can be used to
pass n argument to p.adjusted calculations.
Changes in version 0.0.0.9023
- fixes handling NAs when counting variables occurences. Previously
presence of NA in any allele was ignored and all not observed
alleles were treated as so. Now in cases when both alleles are NA
this is reflected in counts. However if only one of the alleles is
missing behaviour is still the same as previously. The described new
behaviour is spread to hlaToVariable and getHlaKirInteractions
functions.
Changes in version 0.0.0.9022
- bahvior of variables argument in analyzeMiDASData is now changed,
such that it can be used to supply additional variables to analyse
that cannot be selected by analysis_type
Changes in version 0.0.0.9021
- changes the behaviour of analyzeMiDASData conditional = TRUE. Now it
return list of results from all iterations and kables only best
results from each iteration.
Changes in version 0.0.0.9020
- adds human friendly erros in readHlaCalls
Changes in version 0.0.0.9019
- makes it possible to specify na.strings while reading HLA and KIR
calls input files
Changes in version 0.0.0.9018
- fixes a bug when models were accessed and updated in parent frame,
making it error prone in more complex examples. Now modeels are
evaluated in the enviorment they were created in (one defined in
model$terms .Enviorment attribute.
Changes in version 0.0.0.9017
- adds kir_genes analysis type to prepareMiDASData and
analyzeMiDASData
- adds hla_kir_interactions analysis type to prepareMiDASData and
analyzeMiDASData
Changes in version 0.0.0.9016
- adds checkKirCountsFormat to assert KIR counts format
- adds getHlaKirInteractions to get HLA - KIR interactions as new
variables
- add new function MiDAS that combines prepareMiDASData and
analyzeMiDASData.
- result returned by MiDAS stores its input hla_calls and transformed
data in corresponding attributes allowing transformed data to be
reused in subsequent analyzes.
Changes in version 0.0.0.9015
- adds kirHaplotypeToCounts for converting KIR halplotypes to genes
counts
- adds readKirCalls that allows parsing KIR haplotypes calls output by
kpi (https://github.com/droe-nmdp/kpi)
Changes in version 0.0.0.9014
- in analyzeMiDASData now it is possible to specify both lower and
upper threshold on frequency, before it was only lower.
Changes in version 0.0.0.9013
- prepareMiDASData now can accept multiple analysis types at once
which allows to cerate data frames with all possible variables in
one go
- variables in data frame produced by prepareMiDASData are now labeled
with corresponding analysis type
- analyzeMiDASData now under variables = NULL selects appropaite
variables based on labels associated with midas_data
Changes in version 0.0.0.9012
- fixes analyzeMiDASData function crashing on float variables. Now
frequency calculations are done only for properly labeled variables
on midas_data.
Changes in version 0.0.0.9011
- fixes allele_group preparation scheme, where before after conversion
to groups there were no conversion to counts. Additionally now this
scheme have been broken into three: allele_g_group,
allele_supertypes, allele_group (Bw4/6, C1/2).
Changes in version 0.0.0.9010
- introduces prepareMiDASData which transforms hla_calls according to
predefined schemas, like amino acid variation, expression level etc.
Changes in version 0.0.0.9009
- adds script for conversion of HLA calls to VCF format
- adds script for conversion of VCF to HLA calls
Changes in version 0.0.0.9008
- introduces countsToHlaCalls that allows converting HLA counts table
back to HLA calls data frame under additive inheritance model
- introduces analyzeMiDASData which is a higher level abstraction of
analyzeConditionalAssociations and analyzeAssociations. It also
pretty format results to kabled html or latex.
- introduces formatResults that allows to format results to kabled
html ir latex.
Changes in version 0.0.0.9007
- forwardConditionalSelection has been renamed to
analyzeConditionalAssociations, now it returns tibble containing
results from conditional testing as the new covariates are beeing
added. For each variable results from the test upon which the
variable is used for the first time are showed.
- Warnings about uninitialized variables comming from dplyr functions
has been solved.
Changes in version 0.0.0.9006
- analyzing associations and stepwise selection now has been rewriten
such that they operate on model objects returned by functions such
as lm. The amount of inputs is minimized to only variables that are
to be analyzed.
- hlaAssocModels function has been removed as it became obsolete.
- hlaToAAVariation now returns data frame by default, matrix still can
be returned for now if specified.
- Functions for calculation alleles and amino acids frequencies were
added.
- Function for converting amino acids data frame have been added.
Changes in version 0.0.0.9005
- now hla calls are merged with phenotypic and covariate data before
using statistical functions, using prepareHlaData. This workflow is
going to be further strenghtend in future releases.
- introduce inheritance models specifying how hla calls should be
converted to hla counts.
- Response and covariate variables in statistical functions now have
to be typed by hand.
Changes in version 0.0.0.9004
- introduce forwardConditionalSelection for stepwise conditional
testing, adding the previous top-associated allele as covariate,
until there’s no more significant alleles
Changes in version 0.0.0.9003
- G groups alleles are now accepted as properly formatted
- G groups alleles can be now reduced, with warning
Changes in version 0.0.0.9002
- introduce analyzeHlaAssociations for performing statistical analysys
of HLA alleles associations
Changes in version 0.0.0.9001
- added functions for converting alleles into additional variables
Changes in version 0.0.0.9000
- Begining of the CHANGELOG