aed_compare

ingenannot aed_compare generate graphs for AED comparison between different annotation sources.

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>.

outputs

The output consist of 3 graphics, showing cumulative distributions of aed scores for transcripts, proteins or best of both for all sources of dataset available in the FoF. These graphics allow comparison of aed score between datasets. You can compute some metrics as … with –statistics

Output example of plot showing cumulative transcript aed scores:

cumulative AED plot

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).