aed_compare
Command aed_compare generates graphs and computes statistics for AED comparison between different sources of annotations.
usage
$ ingenannot -v 2 aed_compare file.fof
positional arguments:
FoF |
File of files, <GFF/GTF>TAB<source> |
optional arguments:
-h, –help |
show this help message and exit |
-s, –statistics |
Perform statistics on AED scores between sources , default=False |
inputs
File of Files (FoF) with all files to compare. One per line such: <GFF/GTF>TAB<source>.
# write compare.fof
src1.aed.gff<TAB>run1
src2.aed.gff<TAB>run2
src3.aed.gff<TAB>run3
outputs
The output is three graphs, showing cumulative distributions of AED scores for transcripts, proteins or best of both for all sources of dataset available in the FoF. These graphs allow comparison of AED scores between datasets. You can compute some metrics with –statistics
Output example of plot showing cumulative transcript AED scores:
Output of statistics:
# |
mean (tr) |
median (tr) |
stdev (tr) |
mean (pr) |
median (pr) |
stdev (pr) |
median_geom_x |
median_geom_y |
mean_distance |
mean_distance_to_0 |
median_distance |
median_distance_to_0 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
run1 |
0.244 |
0.152 |
0.258 |
0.478 |
0.176 |
0.480 |
0.176 |
0.238 |
0.515 |
0.296 |
0.287 |
0.296 |
run2 |
0.239 |
0.138 |
0.255 |
0.444 |
0.089 |
0.476 |
0.154 |
0.160 |
0.495 |
0.222 |
0.216 |
0.222 |
run3 |
0.171 |
0.030 |
0.273 |
0.551 |
1.000 |
0.482 |
0.144 |
0.656 |
0.537 |
0.671 |
0.567 |
0.671 |
Basic metrics as mean, median and stdev are provided, as well as geometric median and distance of all transcripts to this median or distance to the ideal point (0,0).