Man pages for wefang/ghelper
Genomics Helper Functions
| align2bin | Newer version of alignemnt object to counts |
| align2region | Newer version of alignemnt object to count over regions |
| aveMatFac | Average matrix rows based on a factor |
| bam2bin | Convert bam files to bin counts |
| bin2bp | Convert bin indices to base pair indices |
| bp2bin | Convert base pair indices to bin indices |
| chr2gw | Convert chromosome bin indices to genome wide bin indices. |
| chr2num | Convert seqnames to numeric chromosome indices. Old. For the... |
| countReads | Count reads in bins from GeonomicAlignments object. |
| df2bin | Convert reads saved as list of data.frames to counts |
| df2region | Count overlaps of regions and read centers |
| empirical.pvalue | Calculate empirical p-values |
| gw2chr | Convert vector of genome wide bin indices to a list of... |
| import.broadPeak | Imports broadPeak files |
| import.narrowPeak | Imports narrowPeak files |
| list2gw | Convert a list of indices per chromosome (must have 23 items... |
| load.chrlen | Load chromosome length and bin counts into global environment |
| make_gr_bins | Create a 'GRanges' object for bins. |
| perm.mat | Permutate columns of matrix independently |
| perm.mat.multi | Permutate columns of multiple matrix independently |
| seq2num | Convert seqnames to numeric chromosome indices. chrX mapped... |
| str_to_gr | Convert string to GR object |
| sumMatFac | Sum matrix rows based on a factor |
| ta2bin | Convert tagAlign files to bin counts |
