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methylcheck EPICv2 array implementation #83

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c0632e2
methylcheck integrating EPICv2 data types on pipeline
aregano Nov 18, 2025
37424e4
methylcheck integrating EPICv2 data types on pipeline
aregano Nov 18, 2025
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2 changes: 2 additions & 0 deletions methylcheck/QCreport.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
# -*- coding: utf-8 -*-

11 changes: 8 additions & 3 deletions methylcheck/cli.py
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Expand Up @@ -47,9 +47,12 @@ def get_filename(array_name):
if on_lambda:
man_path = Path(MANIFEST_DIR_PATH_LAMBDA).expanduser()
else:
man_path = Path(MANIFEST_DIR_PATH).expanduser()
man_filename = ARRAY_FILENAME[array_name]
man_filepath = Path(man_path, man_filename)
if array_name == "epicv2":
man_path = "../software/MethylationEPIC_v2.0" # location of the epicv2 manifest file
else:
man_path = Path(MANIFEST_DIR_PATH).expanduser()
man_filename = ARRAY_FILENAME[array_name]
man_filepath = Path(man_path, man_filename)
return man_filepath

# shape: should be wide, with more columns than rows. The larger dimension is the probe count.
Expand All @@ -66,6 +69,8 @@ def get_filename(array_name):
return 'epic+' if returns == 'name' else (ArrayType('epic+'), get_filename('epic+'))
elif 860000 <= col_count <= 868000: # actual: 865860
return 'epic' if returns == 'name' else (ArrayType('epic'), get_filename('epic'))
elif 868001 <= col_count <= 1999999: # actual: 990k approx
return 'epic' if returns == 'name' else (ArrayType('epicv2'), get_filename('epicv2'))
elif 200000 <= col_count <= 300000: # actual: 236685 C20, 262812 v2, 284762 V3-V4, MM285 293220 --- testing, changed max from 270k to 290k for v1.4.6
return 'mouse' if returns == 'name' else (ArrayType('mouse'), get_filename('mouse'))
else:
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Binary file added methylcheck/data_files/EPICv2_control.npy
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Binary file added methylcheck/data_files/EPICv2_sex.npy
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