Skip to content
GitLab
Projects
Groups
Snippets
Help
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in / Register
Toggle navigation
Open sidebar
VEBER Philippe
codepi
Commits
0d01bb24
Commit
0d01bb24
authored
Nov 03, 2020
by
Philippe Veber
Browse files
added in house LMM in pipeline
parent
dc36ba8c
Changes
5
Hide whitespace changes
Inline
Side-by-side
Showing
5 changed files
with
30 additions
and
1 deletion
+30
-1
app/lmm_benchmark.ml
app/lmm_benchmark.ml
+2
-1
lib/detection_pipeline.ml
lib/detection_pipeline.ml
+7
-0
lib/detection_pipeline.mli
lib/detection_pipeline.mli
+2
-0
lib/inhouse_lmm.ml
lib/inhouse_lmm.ml
+12
-0
lib/inhouse_lmm.mli
lib/inhouse_lmm.mli
+7
-0
No files found.
app/lmm_benchmark.ml
View file @
0d01bb24
...
...
@@ -4,11 +4,12 @@ let benchmark d =
let
open
Simulation_dataset
in
Utils
.
recall_precision_curve
~
oracle
:
(
oracle
d
)
~
labels
:
[
|
"topological"
;
"multinomial"
;
"gemma_score"
;
"tdg09"
|
]
~
labels
:
[
|
"topological"
;
"multinomial"
;
"gemma_score"
;
"
inhouse"
;
"
tdg09"
|
]
~
results
:
[
topological
d
;
multinomial_asymptotic_lrt
d
;
gemma
~
lmm_test
:
`Score
~
relatedness_mode
:
`Standardized
d
;
inhouse_lmm
d
;
tdg09
d
;
]
...
...
lib/detection_pipeline.ml
View file @
0d01bb24
...
...
@@ -54,6 +54,8 @@ module type S = sig
relatedness_mode
:
[
`Centered
|
`Standardized
]
->
text
file
val
inhouse_lmm
:
query
->
text
file
val
diffsel
:
query
->
text
file
val
diffseldsparse
:
...
...
@@ -173,6 +175,11 @@ module Make (Q : Query) = struct
~
relatedness_matrix
|>
Gemma
.
result_table_of_output
alignment
let
inhouse_lmm
q
=
let
alignment
=
amino_acid_alignment
q
in
let
tree
=
tree
~
branch_length_unit
:
`Amino_acid
q
in
Inhouse_lmm
.
test
alignment
tree
let
diffseltree
d
=
Tree_dataset
.
prepare_diffsel_tree
(
tree
~
branch_length_unit
:
`Amino_acid
d
)
...
...
lib/detection_pipeline.mli
View file @
0d01bb24
...
...
@@ -54,6 +54,8 @@ module type S = sig
relatedness_mode
:
[
`Centered
|
`Standardized
]
->
text
file
val
inhouse_lmm
:
query
->
text
file
val
diffsel
:
query
->
text
file
val
diffseldsparse
:
...
...
lib/inhouse_lmm.ml
0 → 100644
View file @
0d01bb24
open
Phylogenetics
open
Codepitk
let
%
pworkflow
[
@
version
2
]
test
alignment
tree
=
let
alignment
=
Alignment
.
from_fasta
[
%
path
alignment
]
|>
Rresult
.
R
.
get_ok
in
let
tree
=
Convergence_tree
.
from_file
[
%
path
tree
]
in
Inhouse_lmm
.
test
~
alignment
~
tree
|>
Inhouse_lmm
.
result_table_of_test
|>
Result_table
.
to_file
~
output
:
[
%
dest
]
lib/inhouse_lmm.mli
0 → 100644
View file @
0d01bb24
open
Bistro
open
File_formats
val
test
:
aminoacid_fasta
file
->
nhx
file
->
text
file
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment