Man pages for AndersenLab/linkagemapping
Functions for the Mapping of Andersen Lab RIAILs and RILs
| AF16xHK104cross | Cross object for AF16xHK104 C. brggsae RIAILs |
| AF16xHK104markers | Marker/position lookup table for AF16xHK104 RIAILs |
| AllCBfosmids | Dataframe of all CB4856 fosmids in the Andersen Lab |
| AllCBfosmids_pacbio | Dataframe of all CB4856 fosmids in the Andersen Lab -... |
| AllN2fosmids | Dataframe of all N2 fosmids in the Andersen Lab |
| annotate_lods | Annotate LOD peaks with variance explained, effect size, and... |
| calc_mediation | Calculate mediation scores between phenotype and gene... |
| checkeQTLintervals | Find expression QTL from the Rockman dataset within a... |
| count_strains_per_trait | Count number of strains with data for each phenotype from... |
| effectplot | Plot effect size by marker |
| eQTLpeaks | Dataframe of all eQTL peak location information from Matt... |
| eqtlpheno | Expression phenotypes from Rockman 2010 paper, reanalyzed for... |
| extract_genotype | Extract genotype matrix from cross structure and recode as... |
| extract_scaled_phenotype | Extract phenotype matrix from cross object, mean center and... |
| findCBfosmids | Find CB4856 fosmids that tile across a given interval |
| findindels | Find indels to generate primers |
| findN2fosmids | Find N2 fosmids that tile across a given interval |
| FindRIAILsforNILs | Find RIAILs for generating NILs to isolate a genomic region |
| fsearch | Map all of the traits in a given cross object with forward... |
| indels | Dataframe of indels between N2 and CB4856 |
| load_cross_obj | Load Cross Obj |
| lodplot | Plot all lod scores for a forward search mapping by iteration |
| mapformat | Get the LOD value for each marker based on the correlation... |
| maxlodplot | Plot max lod scores for a forward search mapping |
| mergepheno | Merge the cross object and the phenotype data frame using a... |
| N2xCB4856cross | Cross object for N2xCB4856 RIAILs |
| N2xCB4856cross_full | Whole genome cross object for N2xCB4856 RIAILs |
| N2xCB4856markers | Marker/position lookup table for N2xCB4856 RIAILs |
| N2xLSJ2cross | Cross object for N2xLSJ2 RIAILs |
| N2xLSJ2markers | Marker/position lookup table for N2xLSJ2 RIAILs |
| probe_info | Dataframe of GO terms, descriptions, and other information... |
| pxgplot | Plot the phenotype by genotype split at each peak marker in a... |
| pxgplot_par | Plot the phenotype by genotype split at each peak marker in a... |
| RIAILgenotypes | Genotypes of RIAILs at each of the 1454 markers |
| RIAILmarkerconversion | Marker conversions for each of the 1454 markers used in... |
