Version 1.0-x of the ASMap package celebrates the
Journal of Statistical Software publication, Taylor and Butler
(2017). The paper succinctly summarizes the important contents of
the package vignette and provides a useful quick reference for the
functionality of the package. If you use ASMap in your
publication please reference it using the bibliographic reference obtainable using
citation("ASMap") and given below.
Taylor, J., Butler, D. (2017) R Package ASMap: Efficient Genetic Linkage Map Construction and Diagnosis. Journal of Statistical Software, 79(6), 1–29.
There is now a p-value function to emulate Figure 1.1 in
the vignette. The function allows users to specify their own set
of threshold distances and population sizes, making it easier to
determine the correct choice of p.value to use in
mstmap.cross and mstmap.data.frame.
The function combineMap has been updated to include
merging of linkage maps by "marker" or
"genotype". Merging by "genotype" is identical to
the previous version of the function. Merging by
"marker" provides the ability to combine linkage maps with
different sets of genotypes through common markers.
fixClones muddled linkage groups when an inputted map
had more than one linkage group. This has now been amended.
The fixClones function crashed when consensus =
FALSE was set. This has now been amended.
The cross.scheme of the object was lost when pushing
back markers using pushCross. This has now been amended.
The function quickEst crashed when there were linkage
groups with one marker. This has now been amended.
The function alignCross crashed with a non-descript
error when there were no matching markers in supplied reference
maps. This has now been amended to provide a more descript error.
This is the first documented NEWS release of ASMap. For this reason it contains information about features of the package as well as recent bug fixes.
The package now contains a function to assist in identifying
and orienting linkage groups (see ?alignCross).
The heat map in the package now uses a diverging colour palette chosen from the default palettes available in RColorBrewer.
The package now includes a PDF vignette. This can be found on any operating system using the command
> vignette("ASMap")
The vignette includes extensive descriptions of the package functions as well as fully worked example that showcases the package functions throuh pre-diagnosis, construction and post diagnosis of a linkage map. It also describes how the package can be used efficiently for techniques such as fine mapping or combining maps.
The package now includes three fully documented marker data sets for users to explore. See the vignette for more details.
Fixed a nasty bug in combineMap() that switched
genotype names for certain linkage maps
Fixed bug that returned inflated distances for "ARIL"
populations when using mstmap.data.frame().
If the constructed map contained linkage groups with one
marker profileMark() graphically displaced the interval
statistics. This has now been amended.
pushCross() can now push large volumes of co-located
markers back into the constructed map very efficiently.
profileMark() was not outputting crti.val column
when crit.val = "bonf" argument was chosen. This has now
been amended.
quickEst() has been improved and now provides an even
more accurate and efficient distance calculations for linkage maps.