Merge pull request #80 from Sage-Bionetworks/jbeck/AG-1147/test_trans…

…form_rna_seq

AG-1147/AG-1148/AG-1098: Add tests for rna seq data and rna distribution data

src/agoradatatools/etl/transform/__init__.py

@@ -16,9 +16,11 @@
 from agoradatatools.etl.transform.proteomics_distribution import (
     create_proteomics_distribution_data,
 )
+from agoradatatools.etl.transform.rnaseq_differential_expression import (
+    transform_rnaseq_differential_expression,
+)
 from agoradatatools.etl.transform.rna_distribution import (
     transform_rna_distribution_data,
-    transform_rna_seq_data,
 )
 from agoradatatools.etl.transform.team_info import transform_team_info
 
@@ -30,6 +32,6 @@
     "transform_overall_scores",
     "create_proteomics_distribution_data",
     "transform_rna_distribution_data",
-    "transform_rna_seq_data",
+    "transform_rnaseq_differential_expression",
     "transform_team_info",
 ]

src/agoradatatools/etl/transform/rna_distribution.py

@@ -1,52 +1,10 @@
 import numpy as np
-
-
-def transform_rna_seq_data(datasets: dict):
-    diff_exp_data = datasets["diff_exp_data"]
-
-    diff_exp_data["study"].replace(
-        to_replace={"MAYO": "MayoRNAseq", "MSSM": "MSBB"}, regex=True, inplace=True
-    )
-    diff_exp_data["sex"].replace(
-        to_replace={
-            "ALL": "males and females",
-            "FEMALE": "females only",
-            "MALE": "males only",
-        },
-        regex=True,
-        inplace=True,
-    )
-    diff_exp_data["model"].replace(
-        to_replace="\\.", value=" x ", regex=True, inplace=True
-    )
-    diff_exp_data["model"].replace(
-        to_replace={"Diagnosis": "AD Diagnosis"}, regex=True, inplace=True
-    )
-    diff_exp_data["fc"] = 2 ** diff_exp_data["logfc"]
-    diff_exp_data["model"] = diff_exp_data["model"] + " (" + diff_exp_data["sex"] + ")"
-
-    diff_exp_data = diff_exp_data[
-        [
-            "ensembl_gene_id",
-            "hgnc_symbol",
-            "logfc",
-            "fc",
-            "ci_l",
-            "ci_r",
-            "adj_p_val",
-            "tissue",
-            "study",
-            "model",
-        ]
-    ]
-
-    return diff_exp_data
-
+from agoradatatools.etl import transform
 
 def transform_rna_distribution_data(datasets: dict):
     # "datasets" contains the unprocessed RNA-seq data, which needs to go
     # through the same processing as before in order to use it here.
-    rna_df = transform_rna_seq_data(datasets)
+    rna_df = transform.transform_rnaseq_differential_expression(datasets)
     rna_df = rna_df[["tissue", "model", "logfc"]]
 
     rna_df = (

src/agoradatatools/etl/transform/rnaseq_differential_expression.py

@@ -0,0 +1,40 @@
+def transform_rnaseq_differential_expression(datasets: dict):
+    diff_exp_data = datasets["diff_exp_data"]
+
+    diff_exp_data["study"].replace(
+        to_replace={"MAYO": "MayoRNAseq", "MSSM": "MSBB"}, regex=True, inplace=True
+    )
+    diff_exp_data["sex"].replace(
+        to_replace={
+            "ALL": "males and females",
+            "FEMALE": "females only",
+            "MALE": "males only",
+        },
+        regex=True,
+        inplace=True,
+    )
+    diff_exp_data["model"].replace(
+        to_replace="\\.", value=" x ", regex=True, inplace=True
+    )
+    diff_exp_data["model"].replace(
+        to_replace={"Diagnosis": "AD Diagnosis"}, regex=True, inplace=True
+    )
+    diff_exp_data["fc"] = 2 ** diff_exp_data["logfc"]
+    diff_exp_data["model"] = diff_exp_data["model"] + " (" + diff_exp_data["sex"] + ")"
+
+    diff_exp_data = diff_exp_data[
+        [
+            "ensembl_gene_id",
+            "hgnc_symbol",
+            "logfc",
+            "fc",
+            "ci_l",
+            "ci_r",
+            "adj_p_val",
+            "tissue",
+            "study",
+            "model",
+        ]
+    ]
+
+    return diff_exp_data

src/agoradatatools/process.py

@@ -35,7 +35,7 @@ def apply_custom_transformations(datasets: dict, dataset_name: str, dataset_obj:
     if dataset_name == "team_info":
         return transform.transform_team_info(datasets=datasets)
     if dataset_name == "rnaseq_differential_expression":
-        return transform.transform_rna_seq_data(datasets=datasets)
+        return transform.transform_rnaseq_differential_expression(datasets=datasets)
     if dataset_name == "gene_info":
         return transform.transform_gene_info(
             datasets=datasets,

tests/test_assets/rna_distribution_data/input/test_rna_distribution_data_bad_input_keyerror.csv

@@ -0,0 +1,7 @@
+model,tissue,comparison,ensembl_gene_id,logfc,ci_l,ci_r,aveexpr,t,p_value,adj_p_val,gene_biotype,chromosome_name,direction,hgnc_symbol,percentage_gc_content,gene_length,sex,study
+,CBE,AD-CONTROL,ENSG00000228521,1.646715414,1.219378549,2.074052279,-2.452298708,7.544599094,2.21E-13,2.26E-10,lncRNA,7,UP,AC099552.3,60.6903164,1043,ALL,MAYO
+,CBE,AD-CONTROL,ENSG00000286872,-0.181247795,-0.341187573,-0.021308017,0.032732484,-2.226401902,0.026439738,0.06693269,lncRNA,15,NONE,AC024270.5,46.5131873,13422,ALL,MAYO
+,CBE,AD-CONTROL,ENSG00000144228,0.080531879,-0.016465937,0.177529695,4.913442808,1.63093857,0.10355023,0.193939662,protein_coding,2,NONE,SPOPL,36.67609796,71747,ALL,MAYO
+Diagnosis.AOD,,AD-CONTROL,ENSG00000005339,0.074072272,0.042805132,0.105339413,7.626719604,4.656313999,4.15E-06,8.32E-05,protein_coding,16,NONE,CREBBP,45.00523533,155673,ALL,MAYO
+Diagnosis.AOD,,AD-CONTROL,ENSG00000188994,0.03375383,-0.010318552,0.077826212,6.703806497,1.501322866,0.133920382,0.239511453,protein_coding,6,NONE,ZNF292,37.67626491,113111,ALL,MAYO
+Diagnosis.AOD,,AD-CONTROL,ENSG00000261823,-0.008434191,-0.077650231,0.060781849,-0.970547902,-0.239149259,0.811089637,0.873760793,lncRNA,15,NONE,AC084782.2,42.13615023,1704,ALL,MAYO

tests/test_assets/rna_distribution_data/input/test_rna_distribution_data_bad_input_typeerror.csv

@@ -0,0 +1,2 @@
+model,tissue,comparison,ensembl_gene_id,logfc,ci_l,ci_r,aveexpr,t,p_value,adj_p_val,gene_biotype,chromosome_name,direction,hgnc_symbol,percentage_gc_content,gene_length,sex,study
+Diagnosis,CBE,AD-CONTROL,ENSG00000228521,No change,1.219378549,2.074052279,-2.452298708,7.544599094,2.21E-13,2.26E-10,lncRNA,7,UP,AC099552.3,60.6903164,1043,ALL,MAYO

tests/test_assets/rna_distribution_data/input/test_rna_distribution_data_good_input.csv

@@ -0,0 +1,26 @@
+model,tissue,comparison,ensembl_gene_id,logfc,ci_l,ci_r,aveexpr,t,p_value,adj_p_val,gene_biotype,chromosome_name,direction,hgnc_symbol,percentage_gc_content,gene_length,sex,study
+Diagnosis,CBE,AD-CONTROL,ENSG00000228521,1.646715414,1.219378549,2.074052279,-2.452298708,7.544599094,2.21E-13,2.26E-10,lncRNA,7,UP,AC099552.3,60.6903164,1043,ALL,MAYO
+Diagnosis,CBE,AD-CONTROL,ENSG00000286872,-0.181247795,-0.341187573,-0.021308017,0.032732484,-2.226401902,0.026439738,0.06693269,lncRNA,15,NONE,AC024270.5,46.5131873,13422,ALL,MAYO
+Diagnosis,CBE,AD-CONTROL,ENSG00000144228,0.080531879,-0.016465937,0.177529695,4.913442808,1.63093857,0.10355023,0.193939662,protein_coding,2,NONE,SPOPL,36.67609796,71747,ALL,MAYO
+Diagnosis,CBE,AD-CONTROL,ENSG00000285778,0.011774265,-0.225427841,0.248976371,-1.286000104,0.097352193,0.922486354,0.950960873,lncRNA,1,NONE,AL591463.1,36.23399051,127971,ALL,MAYO
+Diagnosis.AOD,CBE,AD-CONTROL,ENSG00000005339,0.074072272,0.042805132,0.105339413,7.626719604,4.656313999,4.15E-06,8.32E-05,protein_coding,16,NONE,CREBBP,45.00523533,155673,ALL,MAYO
+Diagnosis.AOD,CBE,AD-CONTROL,ENSG00000188994,0.03375383,-0.010318552,0.077826212,6.703806497,1.501322866,0.133920382,0.239511453,protein_coding,6,NONE,ZNF292,37.67626491,113111,ALL,MAYO
+Diagnosis.AOD,CBE,AD-CONTROL,ENSG00000261823,-0.008434191,-0.077650231,0.060781849,-0.970547902,-0.239149259,0.811089637,0.873760793,lncRNA,15,NONE,AC084782.2,42.13615023,1704,ALL,MAYO
+Diagnosis.Sex,CBE,AD-CONTROL,ENSG00000146733,0.245221101,0.088916757,0.401525444,3.6245628,3.081227128,0.002180227,0.025429476,protein_coding,7,NONE,PSPH,46.3530108,40554,FEMALE,MAYO
+Diagnosis.Sex,CBE,AD-CONTROL,ENSG00000164574,0.111683536,-0.075953728,0.299320799,4.556619644,1.16706539,0.24377083,0.459714102,protein_coding,5,NONE,GALNT10,44.28655187,230255,FEMALE,MAYO
+Diagnosis.Sex,CBE,AD-CONTROL,ENSG00000105127,0.036793733,-0.059745776,0.133333242,4.795637019,0.751265208,0.452857433,0.660329327,protein_coding,19,NONE,AKAP8,53.23691982,26414,FEMALE,MAYO
+Diagnosis.Sex,CBE,AD-CONTROL,ENSG00000205790,0.347641938,0.137145533,0.558138342,-0.677376322,3.255063005,0.001212908,0.010745247,lncRNA,19,UP,DPP9-AS1,59.2620369,6667,MALE,MAYO
+Diagnosis.Sex,CBE,AD-CONTROL,ENSG00000171469,-0.147816242,-0.269059529,-0.026572954,3.644836924,-2.399058545,0.016813764,0.066411124,protein_coding,19,NONE,ZNF561,44.45249743,16557,MALE,MAYO
+Diagnosis.Sex,CBE,AD-CONTROL,ENSG00000064703,-0.055752044,-0.165988677,0.054484588,3.592526425,-0.996676453,0.319418656,0.497558937,protein_coding,1,NONE,DDX20,40.26340546,12756,MALE,MAYO
+Diagnosis,FP,AD-CONTROL,ENSG00000260751,-0.247109844,-0.416792039,-0.077427649,0.47017593,-2.856419551,0.004377501,0.037095362,lncRNA,16,NONE,AC008870.2,43.65234375,1024,ALL,MSSM
+Diagnosis,FP,AD-CONTROL,ENSG00000170017,0.116124024,0.013752868,0.218495179,7.605164653,2.220609241,0.026685651,0.111182878,protein_coding,3,NONE,ALCAM,35.28991581,209992,ALL,MSSM
+Diagnosis,FP,AD-CONTROL,ENSG00000235290,-0.057859204,-0.252212735,0.136494327,-0.16909436,-0.584873994,0.558811376,0.712709557,unprocessed_pseudogene,6,NONE,HLA-W,53.26582278,1975,ALL,MSSM
+Diagnosis,FP,AD-CONTROL,ENSG00000177728,0.017353424,-0.086789821,0.12149667,6.788782124,0.32609337,0.744427926,0.845969576,protein_coding,17,NONE,TMEM94,52.00188889,59294,ALL,MSSM
+Diagnosis.Sex,FP,AD-CONTROL,ENSG00000172780,-0.434385421,-0.717838177,-0.150932665,0.396064873,-3.00527216,0.00271497,0.065139157,protein_coding,3,NONE,RAB43,50.78477564,35233,MALE,MSSM
+Diagnosis.Sex,FP,AD-CONTROL,ENSG00000269054,-0.155588882,-0.396743565,0.0855658,0.942597545,-1.265404041,0.206045462,0.491878373,lncRNA,19,NONE,AC012313.6,56.27619238,5011,MALE,MSSM
+Diagnosis.Sex,FP,AD-CONTROL,ENSG00000197497,0.079706407,-0.081429533,0.240842348,2.881636183,0.973898187,0.33048948,0.611179707,protein_coding,19,NONE,ZNF665,45.25955405,34174,MALE,MSSM
+Diagnosis.Sex,FP,AD-CONTROL,ENSG00000155827,0.02916353,-0.045914974,0.104242034,5.680912284,0.768042101,0.442712225,0.699692125,protein_coding,9,NONE,RNF20,38.16967313,29492,MALE,MSSM
+Diagnosis,ACC,AD-CONTROL,ENSG00000125841,-0.181579939,-0.256616609,-0.10654327,6.725621038,-4.743548393,2.22E-06,6.90E-05,protein_coding,20,NONE,NRSN2,51.93726221,12879,ALL,ROSMAP
+Diagnosis,ACC,AD-CONTROL,ENSG00000135898,-0.074241909,-0.471057434,0.322573617,0.222262803,-0.366638152,0.713920945,0.827016898,protein_coding,2,NONE,GPR55,48.82695492,53749,ALL,ROSMAP
+Diagnosis,ACC,AD-CONTROL,ENSG00000151834,-0.027222811,-0.121567916,0.067122295,6.530023004,-0.56550242,0.571784411,0.72424515,protein_coding,4,NONE,GABRA2,35.62900125,226804,ALL,ROSMAP
+Diagnosis.AOD,ACC,AD-CONTROL,ENSG00000099365,-0.093331151,-0.124320202,-0.0623421,8.150447477,-5.901609746,4.10E-09,4.84E-08,protein_coding,16,NONE,STX1B,55.21208437,21383,ALL,ROSMAP

tests/test_assets/rna_distribution_data/input/test_rna_distribution_data_missing_values.csv

@@ -0,0 +1,26 @@
+model,tissue,comparison,ensembl_gene_id,logfc,ci_l,ci_r,aveexpr,t,p_value,adj_p_val,gene_biotype,chromosome_name,direction,hgnc_symbol,percentage_gc_content,gene_length,sex,study
+,CBE,AD-CONTROL,ENSG00000228521,1.646715414,1.219378549,2.074052279,-2.452298708,7.544599094,2.21E-13,2.26E-10,lncRNA,7,UP,AC099552.3,60.6903164,1043,ALL,MAYO
+Diagnosis,CBE,AD-CONTROL,ENSG00000286872,-0.181247795,-0.341187573,-0.021308017,0.032732484,-2.226401902,0.026439738,0.06693269,lncRNA,15,NONE,AC024270.5,46.5131873,13422,ALL,MAYO
+Diagnosis,CBE,AD-CONTROL,ENSG00000144228,0.080531879,-0.016465937,0.177529695,4.913442808,1.63093857,0.10355023,0.193939662,protein_coding,2,NONE,SPOPL,36.67609796,71747,ALL,MAYO
+Diagnosis,CBE,AD-CONTROL,ENSG00000285778,0.011774265,-0.225427841,0.248976371,-1.286000104,0.097352193,0.922486354,0.950960873,lncRNA,1,NONE,AL591463.1,36.23399051,127971,ALL,MAYO
+Diagnosis.AOD,CBE,AD-CONTROL,ENSG00000005339,0.074072272,0.042805132,0.105339413,7.626719604,4.656313999,4.15E-06,8.32E-05,protein_coding,16,NONE,CREBBP,45.00523533,155673,ALL,MAYO
+Diagnosis.AOD,,AD-CONTROL,ENSG00000188994,0.03375383,-0.010318552,0.077826212,6.703806497,1.501322866,0.133920382,0.239511453,protein_coding,6,NONE,ZNF292,37.67626491,113111,ALL,MAYO
+Diagnosis.AOD,CBE,AD-CONTROL,ENSG00000261823,-0.008434191,-0.077650231,0.060781849,-0.970547902,-0.239149259,0.811089637,0.873760793,lncRNA,15,NONE,AC084782.2,42.13615023,1704,ALL,MAYO
+Diagnosis.Sex,CBE,AD-CONTROL,ENSG00000146733,0.245221101,0.088916757,0.401525444,3.6245628,3.081227128,0.002180227,0.025429476,protein_coding,7,NONE,PSPH,46.3530108,40554,FEMALE,MAYO
+Diagnosis.Sex,CBE,AD-CONTROL,ENSG00000164574,0.111683536,-0.075953728,0.299320799,4.556619644,1.16706539,0.24377083,0.459714102,protein_coding,5,NONE,GALNT10,44.28655187,230255,FEMALE,MAYO
+Diagnosis.Sex,CBE,AD-CONTROL,ENSG00000105127,0.036793733,-0.059745776,0.133333242,4.795637019,0.751265208,0.452857433,0.660329327,protein_coding,19,NONE,AKAP8,53.23691982,26414,FEMALE,MAYO
+Diagnosis.Sex,CBE,AD-CONTROL,ENSG00000205790,0.347641938,0.137145533,0.558138342,-0.677376322,3.255063005,0.001212908,0.010745247,lncRNA,19,UP,DPP9-AS1,59.2620369,6667,MALE,MAYO
+Diagnosis.Sex,CBE,AD-CONTROL,ENSG00000171469,-0.147816242,-0.269059529,-0.026572954,3.644836924,-2.399058545,0.016813764,0.066411124,protein_coding,19,NONE,ZNF561,44.45249743,16557,MALE,MAYO
+Diagnosis.Sex,CBE,AD-CONTROL,ENSG00000064703,-0.055752044,-0.165988677,0.054484588,3.592526425,-0.996676453,0.319418656,0.497558937,protein_coding,1,NONE,DDX20,40.26340546,12756,MALE,MAYO
+Diagnosis,FP,AD-CONTROL,ENSG00000260751,-0.247109844,-0.416792039,-0.077427649,0.47017593,-2.856419551,0.004377501,0.037095362,lncRNA,16,NONE,AC008870.2,43.65234375,1024,ALL,MSSM
+Diagnosis,FP,AD-CONTROL,ENSG00000170017,,0.013752868,0.218495179,7.605164653,2.220609241,0.026685651,0.111182878,protein_coding,3,NONE,ALCAM,35.28991581,209992,ALL,MSSM
+Diagnosis,FP,AD-CONTROL,ENSG00000235290,-0.057859204,-0.252212735,0.136494327,-0.16909436,-0.584873994,0.558811376,0.712709557,unprocessed_pseudogene,6,NONE,HLA-W,53.26582278,1975,ALL,MSSM
+Diagnosis,FP,AD-CONTROL,ENSG00000177728,0.017353424,-0.086789821,0.12149667,6.788782124,0.32609337,0.744427926,0.845969576,protein_coding,17,NONE,TMEM94,52.00188889,59294,ALL,MSSM
+Diagnosis.Sex,FP,AD-CONTROL,ENSG00000172780,,-0.717838177,-0.150932665,0.396064873,-3.00527216,0.00271497,0.065139157,protein_coding,3,NONE,RAB43,50.78477564,35233,MALE,MSSM
+Diagnosis.Sex,FP,AD-CONTROL,ENSG00000269054,,-0.396743565,0.0855658,0.942597545,-1.265404041,0.206045462,0.491878373,lncRNA,19,NONE,AC012313.6,56.27619238,5011,MALE,MSSM
+Diagnosis.Sex,FP,AD-CONTROL,ENSG00000197497,,-0.081429533,0.240842348,2.881636183,0.973898187,0.33048948,0.611179707,protein_coding,19,NONE,ZNF665,45.25955405,34174,MALE,MSSM
+Diagnosis.Sex,FP,AD-CONTROL,ENSG00000155827,,-0.045914974,0.104242034,5.680912284,0.768042101,0.442712225,0.699692125,protein_coding,9,NONE,RNF20,38.16967313,29492,MALE,MSSM
+Diagnosis,ACC,AD-CONTROL,ENSG00000125841,-0.181579939,-0.256616609,-0.10654327,6.725621038,-4.743548393,2.22E-06,6.90E-05,protein_coding,20,NONE,NRSN2,51.93726221,12879,ALL,ROSMAP
+Diagnosis,ACC,AD-CONTROL,ENSG00000135898,-0.074241909,-0.471057434,0.322573617,0.222262803,-0.366638152,0.713920945,0.827016898,protein_coding,2,NONE,GPR55,48.82695492,53749,ALL,ROSMAP
+Diagnosis,ACC,AD-CONTROL,ENSG00000151834,-0.027222811,-0.121567916,0.067122295,6.530023004,-0.56550242,0.571784411,0.72424515,protein_coding,4,NONE,GABRA2,35.62900125,226804,ALL,ROSMAP
+Diagnosis.AOD,ACC,AD-CONTROL,ENSG00000099365,-0.093331151,-0.124320202,-0.0623421,8.150447477,-5.901609746,4.10E-09,4.84E-08,protein_coding,16,NONE,STX1B,55.21208437,21383,ALL,ROSMAP

tests/test_assets/rna_distribution_data/output/rna_distribution_data_good_output.json

@@ -0,0 +1,74 @@
+[
+  {
+    "model": "AD Diagnosis (males and females)",
+    "tissue": "ACC",
+    "min": -0.2437,
+    "max": 0.065,
+    "first_quartile": -0.1279,
+    "median": -0.0742,
+    "third_quartile": -0.0507
+  },
+  {
+    "model": "AD Diagnosis x AOD (males and females)",
+    "tissue": "ACC",
+    "min": -0.0933,
+    "max": -0.0933,
+    "first_quartile": -0.0933,
+    "median": -0.0933,
+    "third_quartile": -0.0933
+  },
+  {
+    "model": "AD Diagnosis (males and females)",
+    "tissue": "CBE",
+    "min": -0.7993,
+    "max": 1.2349,
+    "first_quartile": -0.0365,
+    "median": 0.0462,
+    "third_quartile": 0.4721
+  },
+  {
+    "model": "AD Diagnosis x AOD (males and females)",
+    "tissue": "CBE",
+    "min": -0.0492,
+    "max": 0.1158,
+    "first_quartile": 0.0127,
+    "median": 0.0338,
+    "third_quartile": 0.0539
+  },
+  {
+    "model": "AD Diagnosis x Sex (females only)",
+    "tissue": "CBE",
+    "min": -0.0821,
+    "max": 0.3348,
+    "first_quartile": 0.0742,
+    "median": 0.1117,
+    "third_quartile": 0.1785
+  },
+  {
+    "model": "AD Diagnosis x Sex (males only)",
+    "tissue": "CBE",
+    "min": -0.4734,
+    "max": 0.5175,
+    "first_quartile": -0.1018,
+    "median": -0.0558,
+    "third_quartile": 0.1459
+  },
+  {
+    "model": "AD Diagnosis (males and females)",
+    "tissue": "FP",
+    "min": -0.326,
+    "max": 0.2629,
+    "first_quartile": -0.1052,
+    "median": -0.0203,
+    "third_quartile": 0.042
+  },
+  {
+    "model": "AD Diagnosis x Sex (males only)",
+    "tissue": "FP",
+    "min": -0.6259,
+    "max": 0.4424,
+    "first_quartile": -0.2253,
+    "median": -0.0632,
+    "third_quartile": 0.0418
+  }
+]

tests/test_assets/rna_distribution_data/output/rna_distribution_data_missing_data_output.json

@@ -0,0 +1,74 @@
+[
+  {
+    "model": "AD Diagnosis (males and females)",
+    "tissue": "ACC",
+    "min": -0.2437,
+    "max": 0.065,
+    "first_quartile": -0.1279,
+    "median": -0.0742,
+    "third_quartile": -0.0507
+  },
+  {
+    "model": "AD Diagnosis x AOD (males and females)",
+    "tissue": "ACC",
+    "min": -0.0933,
+    "max": -0.0933,
+    "first_quartile": -0.0933,
+    "median": -0.0933,
+    "third_quartile": -0.0933
+  },
+  {
+    "model": "AD Diagnosis (males and females)",
+    "tissue": "CBE",
+    "min": -0.2811,
+    "max": 0.2425,
+    "first_quartile": -0.0847,
+    "median": 0.0118,
+    "third_quartile": 0.0462
+  },
+  {
+    "model": "AD Diagnosis x AOD (males and females)",
+    "tissue": "CBE",
+    "min": -0.0497,
+    "max": 0.1153,
+    "first_quartile": 0.0122,
+    "median": 0.0328,
+    "third_quartile": 0.0534
+  },
+  {
+    "model": "AD Diagnosis x Sex (females only)",
+    "tissue": "CBE",
+    "min": -0.0821,
+    "max": 0.3348,
+    "first_quartile": 0.0742,
+    "median": 0.1117,
+    "third_quartile": 0.1785
+  },
+  {
+    "model": "AD Diagnosis x Sex (males only)",
+    "tissue": "CBE",
+    "min": -0.4734,
+    "max": 0.5175,
+    "first_quartile": -0.1018,
+    "median": -0.0558,
+    "third_quartile": 0.1459
+  },
+  {
+    "model": "AD Diagnosis (males and females)",
+    "tissue": "FP",
+    "min": -0.3508,
+    "max": 0.1781,
+    "first_quartile": -0.1525,
+    "median": -0.0579,
+    "third_quartile": -0.0203
+  },
+  {
+    "model": "AD Diagnosis x Sex (males only)",
+    "tissue": "FP",
+    "min": null,
+    "max": null,
+    "first_quartile": null,
+    "median": null,
+    "third_quartile": null
+  }
+]

tests/test_assets/rnaseq_differential_expression/input/test_rnaseq_differential_expression_bad_input.csv

@@ -0,0 +1,2 @@
+model,tissue,comparison,ensembl_gene_id,logfc,ci_l,ci_r,aveexpr,t,p_value,adj_p_val,gene_biotype,chromosome_name,direction,hgnc_symbol,percentage_gc_content,gene_length,sex,study
+Diagnosis.AOD,TCX,AD-CONTROL,ENSG00000122965,No change,-0.00786889,0.040130378,5.039925164,1.326614942,0.185257779,0.264418818,protein_coding,12,NONE,RBM19,50.4271733,149588,ALL,MAYO