Description Usage Arguments Value Examples
View source: R/exported_functions.R
Clustering at high LOD scores results in marker clusters representing homologues.
bridgeHomologues
clusters these (pseudo)homologues to linkage groups using linkage information between 1.0 and
bridge markers within a parent (e.g. 2.0 for a tetraploid).
If parent-specific bridge markers (e.g. 2.0) cannot be used, biparental markers can also be used (e.g. 1.1, 1.2, 2.1, 2.2 and 1.3 markers).
The linkage information between 1.0 and biparental markers can be combined.
1 2 3 |
cluster_stack |
A |
cluster_stack2 |
Optional. A |
linkage_df |
A linkage |
linkage_df2 |
Optional. A |
LOD_threshold |
Integer. The LOD threshold specifying at which LOD score a link between 1.0 and bridge (e.g. 2.0) markers is used for clustering homologues. |
automatic_clustering |
Logical. Should clustering be executed without user input? |
LG_number |
Integer. Expected number of chromosomes (linkage groups) |
parentname |
Name of the parent. Used in the main title of the plot. |
min_bridges |
The minimum number of cross-parent bridges for a link to be considered.
Make this number higher if there are a lot of spurious links.
This argument is only used for biparental bridges (N.B. if |
log |
Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout. |
A data.frame with markers classified by homologue and linkage group.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | data("P1_homologues", "P2_homologues", "SN_DN_P1", "SN_SS_P1", "SN_SS_P2")
ChHomDf<-bridgeHomologues(cluster_stack = P1_homologues[["5"]],
linkage_df=SN_DN_P1,
LOD_threshold=4,
automatic_clustering=TRUE,
LG_number=5,
parentname="P1")
ChHomDf<-bridgeHomologues(cluster_stack = P1_homologues[["5"]],
cluster_stack2 = P2_homologues[["5"]],
linkage_df=SN_SS_P1,
linkage_df2=SN_SS_P2,
LOD_threshold=4,
automatic_clustering=TRUE,
LG_number=5,
parentname="P1")
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.