Man pages for polymapR
Linkage Analysis in Outcrossing Polyploids

add_dup_markersAdd duplicate markers to a map
ALL_dosagesA dosage matrix for a random pairing tetraploid with five...
all_linkages_list_P1A (nested) list of linkage data frames classified per linkage...
assign_linkage_groupAssign non-SN markers to a linkage group and homologue(s).
assign_SN_SNAssign (leftover) 1.0 markers
bridgeHomologuesUse bridge markers to cluster homologues into linkage groups
calcPotShiftsCalculate potential shifts in marker dosages
calcSegtypeInfoBuild a list of segregation types
checkF1Identify the best-fitting F1 segregation types
check_mapCheck the quality of a linkage map using heatplots
check_marker_assignmentCheck for consistent marker assignment between both parents
cluster_per_LGCluster 1.0 markers into correct homologues per linkage group
cluster_SN_markersCluster 1.0 markers
colour.barAdd colour bar scale to heatplot
consensus_LG_assignmentConsensus LG assignment
consensus_LG_namesFind consensus linkage group names
convert_marker_dosagesConvert marker dosages to the basic types.
correctDosagesCheck if dosage scores may have to be shifted
createChmHomListUser interface for specifying linkage group for a homologue
createMapMarker ordering function
create_phased_maplistCreate a phased homologue map list using the original dosages
createTetraOriginInputCreate input files for TetraOrigin using an integrated...
define_LG_structureGenerate linkage group and homologue structure of SxN markers
finish_linkage_analysisLinkage analysis between all markertypes within LG.
get_markertype_combinationsVisualize and get all markertype combinations for which there...
homologue_lg_assignmentAssign markers to linkage groups and homologues.
integrated.maplistA nested list with integrated maps
leftstrGet substrings from the lefthand side
LGHomDf_P1_1A 'data.frame' specifying the assigned homologue and linkage...
linkageCalculate recombination frequency, LOD and phase
maplist_P1A list of maps of one parent
marker_binningPerform binning of markers.
marker_binning_listBin markers that are in a nested list
marker_data_summarySummarize marker data
MDSMap_from_listWrapper function for MDSMap to generate linkage maps from...
merge_homologuesMerge homologues
merge_marker_assignmentsMerge marker assignments
ModeCalculate the mode of a vector
orient_and_merge_mapsAlign and integrate maps
overviewSNlinksPlotting 1.0 links between homologues
P1_homologuesA list of cluster stacks at different LOD scores
P1_SxS_AssignedA 'data.frame' with marker assignments
p4_functionsCalculate recombination frequency, LOD and log-likelihood...
parental_quantitiesCalculate frequency of each markertype.
PCA_progenyPerform a PCA on progeny
phased.maplistA list of phased maps
phase_SN_diploidPhase 1.0 markers at the diploid level
plot_hom_vs_LGPlot homologue position versus integrated positions
plot_linkage_dfPlot r versus LOD grouped by phase
plot_mapPlot linkage maps
plot_phased_maplistVisualise the phased homologue maplist
plot_SNlinksPlot links between 1.0 markers
polymapRLinkage analysis in polyploids
prepare_pwdPrepare pwd for mapping scripts e.g. MDSmap
r3_functionsCalculate recombination frequency, LOD and log-likelihood...
r4_functionsCalculate recombination frequency, LOD and log-likelihood...
r6_functionsCalculate recombination frequency, LOD and log-likelihood...
rightstrGet substrings from the righthand side
r_LOD_plotPlot r versus LOD
screen_for_duplicate_individualsScreen for duplicate individuals
screen_for_duplicate_markersScreen for and remove duplicated markers
screen_for_NA_valuesScreen marker data for NA values
segtypeInfoSummarySummarize the segtypeInfo list
selSegtypeInfoRestrict a list of segregation types to specified inheritance...
SNSN_LOD_deviationsIdentify deviations in LOD scores between pairs of simplex x...
SN_SN_P1A linkage 'data.frame'.
split_linkage_infoSplit linkage information into homologues
test_cluster_stackError and warning handling for cluster_stack
test_dosage_matrixError and warning handling for dosage_matrix
test_LG_hom_stackError and warning handling for LG_hom_stack
test_linkage_dfError and warning handling for linkage_df
test_prefpairingCheck for and estimate preferential pairing vector or in standardized matrix
write.logheaderWrite a header for the log file
write.mctWrite MapChart file
write_nested_listWrite out a nested list
write.pwdWrite a JoinMap compatible .pwd file from linkage data.frame.
write_pwd_listWrite pwd files from a nested list
polymapR documentation built on Feb. 14, 2018, 1:03 a.m.