What's new in this version?
Haplin version 4.1, uploaded March
15, 2012
- The function haplinSlide now provides feedback as it runs. A
new argument, slaveOutfile, can be used to redirect the feedback
to a file.
- A minor bug in the GWAS data conversion caused the conversion
to crash for some types of family structures. This has now been
fixed.
Haplin version 4.0, uploaded Jan
26, 2012
- The main new feature is that Haplin now provides full support
for
GWAS data (through the GenABEL library data structure). Parallel
processing is integrated in the sliding window estimation and is
activated by simply choosing the number of cpus available
(implemented
using the snowfall library).
- A new argument comb.sex to be used with X-chromosome analyses.
It
allows analyses of males and females separately, and different
ways of
combining males and females in a joint analysis, corresponding
to
dose-response models or X-inactivation.
Haplin
version
3.5,
uploaded
May
26,
2010
- A simple GUI for generating syntax available at haplin.fhi.no. NOTE:
implements most
but not all current Haplin features.
- Haplin now accepts data from from the X chromosome, using the
arguments 'xchrom = T' (and 'sex' to specify column for sex
variable).
- Using the 'data.out' argument, haplin can return a processed
version of the original data file, with all haplotypes
estimated/imputed for all families.
- A new function 'haplinSlide' runs haplin on a consecutive
series
of overlapping windows, useful to scan genes with many SNPs.
- A new function 'haptable' creates a useful summary table of
all
the important estimation results from a Haplin run.
- A new function 'haplinTDT' that performs various TDT tests for
comparison. Written by Øivind Skare.
- A new function 'output' which saves tables and figures from a
Haplin run to disk.
Haplin version 3.0.2,
uploaded Jan 11, 2010
- Changes in R release 2.10 relative to 2.9 caused Haplin to
crash
when n.vars > 0. This has now been fixed.
- Some minor fixes in documentation etc.
Haplin version 3.0.1,
uploaded May 27, 2009
- Haplin prepared for upload to the CRAN repository
- Only minor fixes in documentation etc.
Haplin version 3.0,
uploaded April 29, 2009
This is an extensive update, some of the most important
changes
are:
- Implemented as a proper R library. S-Plus version terminated.
- Haplin now handles the combined case-parent triad +
control-parent triad design, and also the standard case-control
design.
- Updated output
- Can choose a multiplicative dose-response model if estimation
of
separate single- and double dose effects is not required
- Killed a number of minor bugs.
Haplin version 2.1.1, uploaded June 12, 2006
- Minor cosmetic changes in printout and in graph appearance.
- Got rid of (most of?) the annoying graphics warnings that
appeared when plotting result
Haplin version 2.1, uploaded May 29, 2006
- Haplin now prints tests of Hardy-Weinberg equilibrium for each
marker separately.
- When
using a reference category (not the default reciprocal
reference)
Haplin 2.0 forgot to print the double dose estimate for the
reference
category, even though it was computed and plotted in the plot.
This has
now been fixed. (Thanks to S. Hussain for pointing this out).
Haplin version 2.0, uploaded Jan 13, 2006
- A change in the format function in the very latest R release
(2.2.0, Oct 06, 2005) caused the R version of Haplin 1.0 to exit
prematurely. This has been fixed in Haplin 2.0.
- This version (finally!) has an option to run with triads
containing missing data through the EM algorithm, by setting
use.missing = T.
- A computation of the standard errors and individual p-values
that
corrects for missing data and ambiguous haplotypes. The
consequence is
that the jackknife resampling used in version 1.0 is no longer
necessary, and
only one run of Haplin is needed. Thus, much less patience is
required
of
the user....
- The initial data handling and sorting is considerably
improved,
with the result that most computations should be faster, and
Haplin can
now handle more SNPs in a run. The exact number of SNPs possible
to run
depends a good deal on the data and population structure, but
6-7 SNPs
should usually run fine.
Haplin version 1.0, uploaded June
1,
2005
- Haplin now uses "reciprocal" as the default reference
category.
This is slightly different from the previous "population" (which
still
can be used by setting reference = "population"). See the
document on
parametrization and reference for more details
- A new "markers" argument that allows the user to select the
markers to be used in the analysis. The user no longer has to
produce
separate data files for each marker selection. See the document
on
Haplin data format for more details
- Much improved handling of rare haplotypes. In the first
(non-numbered) version this selection was rather rough. In
version 1.0
the haplotype frequencies are estimated fairly precisely before
removing the rare haplotypes, leading to less loss of data and
more
precise estimates. The argument "threshold" that determines the
frequency limit for retaining haplotypes is now followed much
more
closely.
- Haplin now prints p-values for all specific effects, and an
overall p-value for the locus
- Haplin now reports the amount of data removed due to
missing genotypes and which families that are removed due to
Mendelian
inconsistencies
- Jackknife resampling procedure (by setting resampling =
"jackknife") adjusts the standard error to compensate for the
missing
information due to unknown haplotypes