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# Readme file for multi-tissue pGWAS/pQTL analyses:
# Oct 2019
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# 1) Overview
We aim to identify protein-QTLs from three tissues after QC.
To do so, we fit the protein-leve (log10-transformed) and GWAS into a linear regression additive model, adjusting for sex, age, and first two genotype-based principal components (PCs) and genotyping platforms (by type [e.g. omni1, omini2.5, NeuroDX]

The implementaion of the linear regression additive model is PLINK2 (v2.00a2LM).


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# 2) File location

## 2a) tissue1_CSF/

### 2a_i) Protein name keys: ForBOX_CSF_afterQC_featureFile.csv

#### 16 variables in this file:
## reference: http://somalogic.com/wp-content/uploads/2017/07/SSM-066-04-SOMAscan-Assay-1.3k-Annotations-Column-Description.pdf
01)SOMAseqID: A inhouse modified SOMAmer sequence identifier unique to a specific SOMAmer reagent.		
02)SeqId: The SOMAmer sequence identifier unique to a specific SOMAmer reagent.	
03)SomaId: The other SOMAmer identifier unique to a specific SOMAmer reagent, starting with SL.	
04)TargetFullName: The full protein name associated with the target protein(s) used in the selection of the SOMAmer reagent.	
05)Target: The short protein name associated with the target protein(s) used in the selection of the SOMAmer reagent.	
06)UniProt: The specific UniProt ID used to pull in the subsequent annotation columns.	
07)EntrezGeneID: Entrez gene ID(s) associated with this protein.	
08)EntrezGeneSymbol: Entrez gene symbols associated with this protein. 	
09)Organism: The organism source the protein measured from (Human/Human papillomavirus type 16/Human papillomavirus type 18/isolate BEN/isolate LW123).	
10)Units: Relative fluorescent units (RFU).	
11)Type: Protein or Non-Human or Rat Protein.	
12)Dilution: Dilution group to which the SOMAmer Reagent belongs in the SOMAscan Assay (in percentage).	
13)PlateScale.Reference: refererence value for the plate scaling normalization step.	
14)CalReference: refererence value for the calibrator scaling normalization step.	
15)ColCheck: SOMAscan official report metrics based upon scale factor. 	
16)Dilution2: Dilution group to which the SOMAmer Reagent belongs in the SOMAscan Assay (in decimal).

### 2a_ii) Summary statistics files labeled with SOMAseqID: *.glm.linear.gz
#### In total, 713 summary statistics files.

#### 12 variables in this file:
## reference: https://www.cog-genomics.org/plink/2.0/formats#glm_linear
01)#CHROM: Chromosome code
02)POS: Base-pair coordinate     
03)ID: Variant ID      
04)REF: Reference allele
05)ALT: All alternate alleles, comma-separated     
06)A1:	Counted allele in regression      
07)TEST: Test identifier    
08)OBS_CT: 	Number of samples in the regression  
09)BETA: Regression coefficient (for A1 allele)    
10)SE: Standard error of log-odds (i.e. beta)      
11)T_STAT: t-statistic for linear regression
12)P: Asymptotic p-value for T-stat




## 2b) tissue2_plasma/
### 2b_i) Protein name keys: ForBOX_plasma_afterQC_featureFile.csv
### 2b_ii) Summary statistics files labeled with SOMAseqID: *.glm.linear.gz
#### In total, 931 summary statistics files.


## 2c) tissue3_brain/
### 2c_i) Protein name keys: ForBOX_brain_afterQC_featureFile.csv
### 2c_ii) Summary statistics files labeled with SOMAseqID: *.glm.linear.gz
#### In total, 1079 summary statistics files.