Man pages for pgpmartin/GeneNeighborhood
Analyze the Neighborhood (Upstream/Downstream Neighbors) of Genes
| analyzeNeighborsOrientation | Analyze the orientation of gene neighbors for a set of... |
| annotationCoverageAroundFeatures | Extract stranded annotation profiles at and around a set of... |
| assembleProfiles | Assemble profiles from the results of the... |
| binFeatureProfiles | Bin coverage profiles given as a matrix or RleList of... |
| coinIndep | Test the independence of 2 sets of distances with the coin... |
| dist2Neighbors | Extract distances to the upstream and downstream neighbors |
| distStats | Descriptive statistics on intergenic distance data |
| distTests | Statistical tests for intergenic distance data |
| extendPointPresence | Extend the presence value (1) of the closest single-point... |
| Genegr | A GRanges with 676 random genes on a single chromosome |
| getAvgProfileWithCI | Compute the average profile and its confidence interval for a... |
| getCumulPercentProfiles | For gene sets, obtain the cumulative percentage of genes with... |
| getDistSide | Filter a gene set and extract upstream or downstream... |
| getGeneNeighborhood | Extract info on upstream and downstream features/genes |
| getTES | Extract the TES (=end of the gene/transcript) from a... |
| getTESregion | Extract a region around the TES (=end of the gene) from a... |
| isBinaryMat | Test if a matrix is a binary matrix |
| ksfun | Kolmogorov-Smirnov test on genomic distances |
| matrix2RleList | Convert an 'matrix' to an 'RleList' |
| plotCumulPercentProfile | Plot the cumulative proportions obtained from... |
| plotDistanceDistrib | plot the distribution of intergenic distances |
| plotMetageneAnnotProfile | Plot metagene annotation profiles for different groups of... |
| plotNeighborsOrientation | Stacked barplot of gene orientations for upstream and... |
| profcomp | Extract windows of interest from a coverage. |
| pvalByGeneSet | Apply a test to different genesets using the same... |
| resampMed | Resampling test on the median (only returns the p-value) |
| RleList2matrix | Convert an 'RleList' to a 'matrix' |
| Utest | Compare 2 sets of distances with a Mann-Whitney U test (only... |
| winsorizeMatrix | Winsorizing of an entire matrix |
