An improvement to bridgeHomologues

24-10-2017

polymapR pipeline

  • Data quality
  • Calculate r and LOD with linkage()
  • Cluster 1x0 markers with cluster_SN_markers()
  • Cluster homologues into chromosomes with bridgeHomologues()

bridgeHomologues - duplex markers

bridgeHomologues - simplex markers

Rose data from workshop

LGHomDf_P2 <- bridgeHomologues(cluster_stack = P2_homologues_5i, 
                               linkage_df = SN_DN_P2,
                               LOD_threshold = 5,
                               LG_number = 7,
                               parentname = "P2")

plot of chunk unnamed-chunk-2

Rose data from workshop

LGHomDf_P2 <- bridgeHomologues(cluster_stack = P2_homologues_5i, 
                               cluster_stack2 = P1_homologues_5,
                               linkage_df = SN_SS_P2,
                               linkage_df2 = SN_SS_P1,
                               LOD_threshold = 5, 
                               LG_number = 7,
                               parentname = "P2")

plot of chunk unnamed-chunk-3

bridgeHomologues2

LGHomDf_P2 <- bridgeHomologues2(cluster_stack = P2_homologues_5i, 
                                linkage_df = SN_DN_P2,
                                LOD_threshold = 4, 
                                automatic_clustering = TRUE, 
                                LG_number = 7,
                                parentname = "P1",
                                min_links = 1,
                                min_bridges = 1)

plot of chunk unnamed-chunk-4


####Unrepresented homologues

|cluster | size|
|:-------|----:|
|10      |   22|
|15      |    8|

bridgeHomologues2

Unrepresented homologues

cluster size
10 22
15 8

bridgeHomologues2

LGHomDf_P2 <- bridgeHomologues2(cluster_stack = P2_homologues_5i, 
                                cluster_stack2 = P1_homologues_5,
                                linkage_df = SN_SS_P2,
                                linkage_df2 = SN_SS_P1,
                                LG_number = 7,
                                parentname = "P2",
                                min_links = 1,
                                min_bridges = 1)

plot of chunk unnamed-chunk-5

bridgeHomologues2

LGHomDf_P2 <- bridgeHomologues2(cluster_stack = P2_homologues_5i, 
                                cluster_stack2 = P1_homologues_5,
                                linkage_df = SN_SS_P2,
                                linkage_df2 = SN_SS_P1,
                                LG_number = 7,
                                parentname = "P2",
                                min_links = 1,
                                min_bridges = 2)

plot of chunk unnamed-chunk-6