Add expression data, sample metadata, and recount2 (#2)

* Add .gitignore

* Add shell script for data download

* Ignore recount2 data from figshare

* Add git LFS tracking pcl

* Add microarray PCL (lfs)

* Add GSE18885 series matrix

* Add sample/phenotype data

* Ignore microarray expression and sample metadata

.gitattributes

@@ -0,0 +1 @@
+*.pcl filter=lfs diff=lfs merge=lfs -text

.gitignore

@@ -0,0 +1,33 @@
+# Ignore hidden metadata files
+._*
+
+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# knitr and R markdown default cache directories
+/*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# Rplot default output
+Rplots.pdf
+
+# recount2 data from figshare
+data/recount2_PLIER_data
+
+# other data from greenelab/rheum-plier-data
+data/expression_data
+data/sample_info

00-data_download.sh

@@ -0,0 +1,39 @@
+#!/bin/bash
+
+# set up directories
+mkdir data && mkdir plots && mkdir results && mkdir util
+
+# data directory subdirectories
+cd data && mkdir expression_data
+
+# get recount2 data & model from figshare, source code in 
+# greenelab/rheum-data-plier
+wget https://ndownloader.figshare.com/files/10881866 \
+  -O recount2.zip
+unzip recount2.zip && rm recount2.zip
+
+## microarray data from greenelab/rheum-plier-data
+cd expression_data
+
+# sle-wb data
+wget https://github.com/greenelab/rheum-plier-data/raw/4be547553f24fecac9e2f5c2b469a17f9df253f0/sle-wb/processed/aggregated_data/SLE_WB_all_microarray_QN_zto_before.pcl
+
+# NARES
+wget https://github.com/greenelab/rheum-plier-data/raw/4be547553f24fecac9e2f5c2b469a17f9df253f0/NARES/processed/NARES_SCANfast_ComBat.pcl
+
+# GPA blood dataset (GSE18885)
+wget https://github.com/greenelab/rheum-plier-data/raw/4be547553f24fecac9e2f5c2b469a17f9df253f0/gpa-blood/GSE18885_series_matrix.txt
+
+# isolated blood cell populations from autoimmune conditions
+wget https://github.com/greenelab/rheum-plier-data/raw/4be547553f24fecac9e2f5c2b469a17f9df253f0/isolated-cell-pop/processed/E-MTAB-2452_hugene11st_SCANfast.pcl
+
+# get sample (e.g., phenotype) data
+cd .. && mkdir sample_info && cd sample_info
+# sle-wb sample to dataset of origin data
+wget https://github.com/jaclyn-taroni/rheum-plier-data/raw/4be547553f24fecac9e2f5c2b469a17f9df253f0/sle-wb/processed/sle-wb_sample_dataset_mapping.tsv
+# other/single dataset sample information
+wget https://github.com/greenelab/rheum-plier-data/raw/4be547553f24fecac9e2f5c2b469a17f9df253f0/sle-wb/arrayexpress/E-GEOD-65391/E-GEOD-65391.sdrf.txt
+wget https://github.com/greenelab/rheum-plier-data/raw/4be547553f24fecac9e2f5c2b469a17f9df253f0/isolated-cell-pop/E-MTAB-2452.sdrf.txt
+wget https://github.com/greenelab/rheum-plier-data/raw/4be547553f24fecac9e2f5c2b469a17f9df253f0/sle-wb/arrayexpress/E-GEOD-39088/E-GEOD-39088.sdrf.txt
+wget https://github.com/greenelab/rheum-plier-data/raw/4be547553f24fecac9e2f5c2b469a17f9df253f0/sle-wb/arrayexpress/E-GEOD-78193/E-GEOD-78193.sdrf.txt
+wget https://github.com/greenelab/rheum-plier-data/raw/4be547553f24fecac9e2f5c2b469a17f9df253f0/NARES/NARES_demographic_data.tsv

data/sample_info/NARES_demographic_data.tsv

@@ -0,0 +1,77 @@
+Sample	Disease	Disease_Activity	Batch	Classification	Severity	ANCA	Age	Race	Gender	Ethnicity	Disease_Duration (yrs)	Flares	PGA	BVAS	VDI	Smoking_pkyrs	Smoking_Status	Steroids_daily_pred_mg	Steroids_Cat	Immune_Meds	GC_or_Immune	Nasal_Steroids	Immune_or_Nasal	Any_Immune
+N1004	GPA	Active	1	V3	Severe	MPO	62	White	F	non-Hisp	6	8	4	7	10	5	Former	30	1	None	1	Y	1	1
+N1007	GPA	Inactive	1	V2	Severe	PR3	43	White	M	non-Hisp	5	0	0	0	1	19	Former	0	0	None	0	N	0	0
+N1017	GPA	Never	1	V1	Severe	PR3	64	White	F	non-Hisp	0.75	0	0	0	0	20	Former	5	1	Azathioprine	1	N	1	1
+N1025	Control	Control	1	C1	N/A	Neg	67	White	F	non-Hisp	.	.	.	.	.	25	Former	0	0	None	0	N	0	0
+N1030	Control	Control	1	C2	N/A	Neg	63	White	F	non-Hisp	2	0	.	.	.	40	Former	15	1	None	1	Y	1	1
+N1033	Control	Control	1	C2	N/A	Neg	67	White	M	non-Hisp	1	2	.	.	.	30	Former	15	1	None	1	N	0	1
+N1006	Control	Control	1	C3	N/A	Neg	52	White	M	non-Hisp	.	.	.	.	.	0	Never	0	0	None	0	N	0	0
+N1009	Control	Control	1	C1	N/A	Neg	61	White	F	non-Hisp	.	.	.	.	.	0	Never	0	0	None	0	N	0	0
+N1011	GPA	Inactive	1	V2	Severe	PR3	54	White	M	non-Hisp	3	1	0	0	0	0	Never	0	0	None	0	N	0	0
+N1012	Control	Control	1	C3	N/A	Neg	52	White	F	non-Hisp	.	.	.	.	.	0	Never	15	1	Rituximab	1	N	1	1
+N1014	Control	Control	1	C1	N/A	Neg	59	White	F	non-Hisp	.	.	.	.	.	0	Never	0	0	None	0	N	0	0
+N1015	GPA	Active	1	V3	Limited	PR3	19	White	F	non-Hisp	5	6	3	3	2	0	Never	7	1	Rituximab	1	N	1	1
+N1018	GPA	Inactive	1	V2	Limited	MPO	72	White	F	non-Hisp	10	3	0	0	2	0	Never	0	0	Azathioprine	1	N	1	1
+N1021	GPA	Never	1	V1	Severe	MPO	54	White	M	non-Hisp	4	2	0	0	3	15	Former	40	1	CYC	1	N	1	1
+N1026	GPA	Never	1	V1	Severe	PR3	78	White	F	non-Hisp	6	0	0	0	2	0	Never	0	0	None	0	N	0	0
+N1029	Control	Control	1	C2	N/A	Neg	51	White	M	non-Hisp	2	0	.	.	.	0	Never	0	0	MTX	1	N	1	1
+N1001	GPA	Inactive	2	V2	Limited	PR3	31	White	F	non-Hisp	3	0	0	0	0	0	Never	2.5	1	MTX	1	N	1	1
+N1002	Control	Control	2	C1	N/A	Neg	27	White	M	Hispanic	.	.	.	.	.	0	Never	0	0	None	0	N	0	0
+N1013	GPA	Never	2	V1	Limited	PR3	61	White	M	non-Hisp	17	0	0	0	0	94	Current	0	0	MTX	1	N	1	1
+N1016	GPA	Inactive	2	V2	Limited	PR3	51	White	M	non-Hisp	7	0	0	0	1	0	Never	0	0	None	0	N	0	0
+N1019	Control	Control	2	C1	N/A	Neg	76	White	M	non-Hisp	.	.	.	.	.	40	Former	0	0	None	0	N	0	0
+N1024	GPA	Inactive	2	V2	Severe	PR3	67	White	M	non-Hisp	4	0	0	0	2	20	Former	0	0	MTX	1	N	1	1
+N1027	Control	Control	2	C2	N/A	Neg	69	White	M	non-Hisp	6	2	.	.	.	15	Former	0	0	None	0	N	0	0
+N1028	Control	Control	2	C2	N/A	Neg	40	White	M	non-Hisp	1	0	.	.	.	0	Never	10	1	None	1	N	0	1
+N1031	GPA	Never	2	V1	Severe	PR3	44	White	F	non-Hisp	2	0	0	0	2	5	Former	0	0	MTX	1	N	1	1
+N1032	Control	Control	2	C1	N/A	Neg	47	White	M	non-Hisp	.	.	.	.	.	0	Never	0	0	None	0	N	0	0
+N1034	GPA	Inactive	2	V2	Severe	PR3	48	White	M	non-Hisp	2	0	0	0	0	30	Current	0	0	None	0	N	0	0
+N1036	Control	Control	2	C3	N/A	Neg	39	Asian	M	non-Hisp	.	.	.	.	.	0	Never	0	0	None	0	Y	1	1
+N1037	Control	Control	2	C2	N/A	Neg	44	White	F	non-Hisp	8	.	.	.	.	0	Never	0	0	CYC	1	N	1	1
+N1038	Control	Control	2	C3	N/A	Neg	18	Black	F	Hispanic	.	.	.	.	.	0	Never	0	0	None	0	Y	1	1
+N1040	GPA	Active	2	V3	Limited	PR3	32	White	F	non-Hisp	3	1	2	2	0	0	Never	0	0	MTX	1	N	0	0
+N1041	GPA	Active	2	V3	Severe	MPO	56	White	F	non-Hisp	1.5	1	2	3	3	0	Never	7.5	1	Rituximab	1	Y	1	1
+N1093	Control	Control	3	C2	N/A	Neg	28	White	M	non-Hisp	1.5	0	.	.	0	2	Former	0	0	None	0	N	0	0
+N1003	GPA	Inactive	3	V2	Limited	MPO	63	White	F	non-Hisp	5	0	0	0	5	100	Former	0	0	None	0	Y	1	1
+N1042A	GPA	Active	3	V3	Limited	PR3	42	White	M	non-Hisp	0.3	0	3	4	0	0	Never	50	1	None	1	N	0	1
+N1043B	Control	Control	3	C1	N/A	Neg	38	White	F	non-Hisp	.	.	.	.	.	0	Never	0	0	None	0	N	0	0
+N1044B	GPA	Active	3	V3	Limited	PR3	40	White	M	Hispanic	0.8	0	4	5	2	0	Never	15	1	Azathioprine	1	N	1	1
+N1048B	GPA	Active	3	V3	Severe	PR3	63	White	M	non-Hisp	8	1	5	10	5	50	Former	30	1	Azathioprine	1	N	1	1
+N1050A	GPA	Active	3	V3	Limited	PR3	44	Arabic	F	non-Hisp	0.8	0	1	1	0	0	Never	7.5	1	MTX	1	N	1	1
+N1052A	GPA	Never	3	V1	Severe	PR3	69	White	F	non-Hisp	13	1	0	0	3	7	Former	5	1	MMF	1	N	1	1
+N1053B	GPA	Never	3	V1	Severe	PR3	48	White	M	non-Hisp	5	2	0	0	0	7	Former	0	0	Rituximab	1	N	1	1
+N1055B	GPA	Inactive	3	V2	Limited	PR3	47	White	F	non-Hisp	9	2	0	0	2	0	Never	0	0	None	0	N	0	0
+N1057A	GPA	Never	3	V1	Severe	MPO	75	White	F	non-Hisp	6	3	0	0	3	45	Former	0	0	None	0	N	0	0
+N1058	GPA	Inactive	3	V2	Severe	PR3	29	White	M	non-Hisp	3	2	1	1	0	0	Never	0	0	MTX	1	N	1	1
+N1060	GPA	Never	3	V1	Severe	PR3	58	White	M	non-Hisp	5	1	0	0	0	25	Former	10	1	RTX	1	N	1	1
+N1061	GPA	Active	3	V3	Severe	PR3	55	White	F	non-Hisp	0.5	0	2	9	1	30	Former	30	1	None	1	N	0	1
+N1064	Control	Control	3	C1	N/A	Neg	57	White	M	non-Hisp	.	.	.	.	.	0	Never	0	0	None	0	N	0	0
+N1066	Control	Control	3	C1	N/A	Neg	71	White	M	non-Hisp	.	.	.	.	.	30	Former	0	0	None	0	N	0	0
+N1068	Control	Control	3	C2	N/A	Neg	51	White	M	non-Hisp	.	.	.	.	.	0	Never	0	0	None	0	Y	1	1
+N1069	Control	Control	3	C2	N/A	Neg	51	Black	F	non-Hisp	.	.	.	.	.	0	Never	0	0	MTXINFLIX	1	N	1	1
+N1070	Control	Control	3	C2	N/A	Neg	43	White	M	non-Hisp	.	.	.	.	.	10	Former	5	1	None	1	N	0	1
+N1073	EGPA	"NA"	3	C4	N/A	MPO	56	White	F	non-Hisp	2	0	0	.	0	0	Never	5	1	MTX	1	N	1	1
+N1074	GPA	Inactive	3	V2	Limited	PR3	71	White	M	non-Hisp	11	2	0	0	3	0	Never	0	0	MTX	1	N	1	1
+N1081	Control	Control	3	C1	N/A	Neg	62	White	F	non-Hisp	.	.	.	.	.	0	Never	0	0	None	0	N	0	0
+N1082	Control	Control	3	C2	N/A	Neg	45	White	F	non-Hisp	1	0	.	.	.	0	Never	0	0	None	0	Y	1	1
+N1086	Control	Control	3	C3	N/A	Neg	41	White	M	non-Hisp	.	.	.	.	.	0	Never	0	0	None	0	N	0	0
+N1087	Control	Control	3	C2	N/A	Neg	51	White	M	non-Hisp	0.5	0	.	.	.	0	Never	20	1	MTX	1	N	1	1
+N1088	GPA	Inactive	3	V2	Severe	PR3	23	White	M	non-Hisp	5	1	0	0	2	0	Never	5	1	None	1	N	0	1
+N1091	GPA	Inactive	3	V2	Severe	PR3	64	White	M	non-Hisp	10	7	0	0	5	0	Never	7	1	MMF	1	N	1	1
+N1092	Control	Control	3	C1	N/A	Neg	59	White	F	non-Hisp	.	.	.	.	.	0	Never	0	0	None	0	N	0	0
+N1094	EGPA	"NA"	3	C4	N/A	Neg	63	White	F	non-Hisp	14	4	0	0	5	0	Never	0	0	Azathioprine	1	N	1	1
+N1095	EGPA	"NA"	3	C4	N/A	Neg	52	White	F	non-Hisp	NA	2	0	0	4	0	Never	10	1	Azathioprine	1	N	1	1
+N1096	EGPA	"NA"	3	C4	N/A	MPO	64	White	F	non-Hisp	.	6	0	1	4	0	Never	2	1	MTX	1	N	1	1
+N1097	Control	Control	3	C1	N/A	Neg	66	White	M	non-Hisp	.	.	.	.	.	0	Never	0	0	None	0	N	0	0
+N1098	Control	Control	3	C2	N/A	Neg	59	White	F	non-Hisp	8	.	.	.	.	0	Never	0	0	MTX	1	N	1	1
+N1099	Control	Control	3	C2	N/A	Neg	53	White	M	non-Hisp	3	.	.	.	.	18	Former	20	1	None	1	N	0	1
+N1100	GPA	Active	3	V3	Severe	PR3	43	White	F	non-Hisp	0.1	0	6	8	0	0	Never	60	1	None	1	N	0	1
+N1101	EGPA	"NA"	3	C4	N/A	MPO	68	White	M	non-Hisp	6	4	2	3	1	0	Never	15	1	None	1	N	0	1
+N1102	EGPA	"NA"	3	C4	N/A	MPO	68	White	M	non-Hisp	3	1	1	1	3	30	Former	0	0	MTX	1	N	1	1
+N1103	EGPA	"NA"	3	C4	N/A	Neg	42	White	M	non-Hisp	10	3	0	0	5	0	Never	5	1	MTX	1	N	1	1
+N1104	EGPA	"NA"	3	C4	Severe	MPO	50	White	F	non-Hisp	7	4	4	NA	0	0	Never	50	1	None	1	N	0	1
+N1105	EGPA	"NA"	3	C4	N/A	Neg	28	White	F	non-Hisp	10	9	5	5	5	0	Never	20	1	RTX	1	N	1	1
+N1106	EGPA	"NA"	3	C4	N/A	Neg	73	White	F	non-Hisp	2	1	0	0	5	40	Former	10	1	Azathioprine	1	N	1	1
+N1107	EGPA	"NA"	3	C4	N/A	Neg	70	White	F	non-Hisp	4	1	0	0	1	0	Never	2	1	MMF	1	N	1	1
+N1108	EGPA	"NA"	3	C4	N/A	Neg	56	White	F	non-Hisp	25	4	0	0	4	0	Never	5	1	Azathioprine	1	N	1	1
+N1110	EGPA	"NA"	3	C4	N/A	MPO	38	Asian	M	non-Hisp	5	3	1	1	4	0	Never	8	1	None	1	N	0	1