Man pages for BatchMap
Software for the Creation of High Density Linkage Maps in Outcrossing Species
| add.marker | Creates a new sequence by adding markers. |
| Bonferroni.alpha | Calculates individual significance level to be used to... |
| combine.onemap | Combine OneMap datasets |
| compare | Compare all possible orders (exhaustive search) for a given... |
| create.data.bins | New dataset based on bins |
| create.dataframe.for.plot.outcross | Create a dataframe suitable for a ggplot2 graphic |
| draw.map | Draw a genetic map |
| drop.marker | Creates a new sequence by dropping markers. |
| est_map_hmm_out | C++ routine for multipoint analysis in outcrossing... |
| example.out | Data from a full-sib family derived from two outbred parents |
| find.bins | Allocate markers into bins |
| group | Assign markers to linkage groups |
| make.seq | Create a sequence of markers |
| map | Construct the linkage map for a sequence of markers |
| map_func | Mapping functions Haldane and Kosambi |
| map.overlapping.batches | Mapping overlapping batches |
| marker.type | Informs the segregation patterns of markers |
| onemap-internal | Internal onemap functions |
| order.seq | Search for the best order of markers combining compare and... |
| pick.batch.sizes | Picking optimal batch size values |
| plot.by.segreg.type | Draw a graphic showing the number of markers of each... |
| plot.onemap | Draw a graphic of raw data for any OneMap population |
| plot.onemap.segreg.test | Plot p-values for chi-square tests of expected segregation |
| print.group | Print group result |
| print.onemap.segreg.test | Print segregation test result |
| print.outcross | Print read.outcross result |
| print.rf.2pts | Print twopoint test result |
| print.try | Print try.seq result |
| pseudo.testcross.split | Split a dataset into parent-specific subsets |
| rcd | Rapid Chain Delineation |
| read.mapmaker | Read data from a Mapmaker raw file |
| read.onemap | Read data from all types of progenies supported by OneMap |
| read.outcross | Read data from a full-sib progeny (outcrossing populations) |
| read.outcross2 | Read data from a full-sib progeny (outcrossing populations) |
| record | Recombination Counting and Ordering |
| record.parallel | Recombination Counting and Ordering |
| rf.2pts | Two-point analysis between genetic markers |
| ripple.ord | Update linkage map with alternative orders at all positions |
| ripple.seq | Compares and displays plausible alternative orders for a... |
| ripple.window | Update linkage map with alternative orders at a given... |
| seeded.map | Construct the linkage map for a sequence of markers after... |
| select.segreg | Show markers with/without segregation distortion |
| seriation | Seriation |
| set.map.fun | Defines the default mapping function |
| suggest.lod | Suggests a LOD Score for two point tests |
| test.segregation | test.segregation |
| test.segregation.of.a.marker | test.segregation.of.a.marker |
| try.seq | Try to map a marker into every possible position between... |
| ug | Unidirectional Growth |
| write.map | Write a genetic map to a file |
