Description Usage Arguments Value Examples
View source: R/exported_functions.R
Clustering at one LOD score for all markers does usually not result in correct classification of homologues. Usually there are more clusters of (pseudo)homologues than expected. This function lets you inspect every linkage group separately and allows for clustering at a different LOD threshold per LG.
1 2 3 4 |
LG |
Integer. Linkage group to investigate. |
linkage_df |
A data.frame as output of |
LG_hom_stack |
A |
LOD_sequence |
A numeric or vector of numerics giving LOD threshold(s) at which clustering should be performed. |
modify_LG_hom_stack |
Logical. Should |
nclust_out |
Number of clusters in the output. If there are more clusters than this number only the nclust_out largest clusters are returned. |
network.layout |
Network layout: |
device |
Function of the graphics device to plot to (e.g. |
label.offset |
Offset of labels. Only used if |
cex.lab |
label character expansion. Only for |
log |
Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout. |
... |
Arguments passed to |
A modified LG_hom_stack data.frame
if modify_LG_hom_stack = TRUE
1 2 3 4 5 6 7 8 9 10 11 12 13 | data("SN_SN_P2", "LGHomDf_P2_1")
#take only markers in coupling:
SN_SN_P2_coupl <- SN_SN_P2[SN_SN_P2$phase=="coupling",]
cluster_per_LG(LG = 2,
linkage_df=SN_SN_P2_coupl,
LG_hom_stack=LGHomDf_P2_1,
LOD_sequence=seq(4,10,2),
modify_LG_hom_stack=FALSE,
nclust_out=4,
network.layout="circular",
device=NULL,
label.offset=1.2,
cex.lab=0.75)
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