Fusion filt bug

[jharenza]

Purpose/implementation Section

What scientific question is your analysis addressing?

Update fusion filtering artifact filter

What was your approach?

Replaced GTEx_Recurrent with GTEx in the shell script artifact filter

What GitHub issue does your pull request address?

Fixes d3b-center/ticket-tracker-OPC#507

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

Is there anything that you want to discuss further?

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

Results

What types of results are included (e.g., table, figure)?

What is your summary of the results?

Fusions now being removed are below. In looking back at OpenPBTA, "GTEx_Recurrent" is still in the list, though not being used since it would not match, and GTEX fusions are being retained. Thinking we might want to leave this alone after all, but just remove GTEX altogether from the artifact filtering so there is no confusion.

> sort(setdiff(unique(putv11$FusionName), unique(put_rerun$FusionName)))
  [1] "AC005258.1--ATP6V0C"        "AC005258.1--METRNL"         "AC005258.1--REXO1"          "AC005258.1--RNF126"         "AC005258.1--RPS15"          "AC005258.1--SAP25"         
  [7] "ACER3--CALCOCO2"            "ADAP1--FAM20C"              "ADCY9--AC093525.2"          "ADCY9--ATP6V0C"             "AEBP2--PLEKHA5"             "ANKHD1--ANKHD1"            
 [13] "ANKRD11--ANKRD11"           "ANKRD11--SLC7A5"            "ARHGEF28--AC143336.1/MAP1B" "ATP11A--TEX29"              "B2M--GNAS"                  "BMPR1B--PDLIM5"            
 [19] "BRD1--TRABD"                "BRD9--CLPTM1L"              "BSG--DAZAP1"                "C5orf42--C5orf42"           "CAMK1D--CDC123"             "CD81--LSP1"                
 [25] "CD81--OSBPL5"               "CD81--SLC7A5"               "CDKN1A--UBC"                "CNN2--RNF126"               "CNOT6L--CCNG2"              "CPSF6--CSNK1D"             
 [31] "CTDP1--MBP"                 "CTDP1--PQLC1"               "CYBA--SLC7A5"               "DAZAP1--REXO1"              "DAZAP1--RNF126"             "DAZAP1--SBNO2"             
 [37] "DENND3--AGO2"               "DNAJC6--PDE1C"              "EGFL7--NOTCH1"              "EIF4A1--OAZ1"               "EIF4A1--SAP25"              "EIF4A1--UBB"               
 [43] "FAM20C--ADAP1"              "FAM20C--PDGFA"              "FGFRL1--CTBP1"              "FRYL--SLAIN2"               "FUBP1--IVNS1ABP"            "GRAMD4--BRD1"              
 [49] "HOXB3--C9orf3"              "HSF2--SERINC1"              "IRS2--ING1"                 "JARID2--PTP4A1"             "KDM4B--DAZAP1"              "LSP1--CD81"                
 [55] "MAEA--GAK"                  "MAFK--ACTB"                 "MAP1LC3B--SLC7A5"           "MBP--CTDP1"                 "MBP--ZNF516"                "MEF2A--LRRC28"             
 [61] "MGRN1--CORO7"               "MGRN1--CORO7-PAM16"         "MGRN1--SLC7A5"              "MTHFS--ST20"                "NCOR1--UBB"                 "NEDD4L--MBP"               
 [67] "NFATC1--PQLC1"              "NKD2--CLPTM1L"              "NUMB--PSEN1"                "OAZ1--ATP6V0C"              "OAZ1--DAZAP1/RPS15"         "OAZ1--KLF16"               
 [73] "OAZ1--KLHL24"               "OAZ1--LPAR2"                "OAZ1--METRNL"               "OAZ1--REXO1"                "OAZ1--RNF126"               "OAZ1--RPS15"               
 [79] "OAZ1--SAP25"                "OAZ1--SBNO2"                "OAZ1--SERINC2"              "OAZ1--UBC"                  "OAZ1--ZBTB7A"               "PCGF3--GAK"                
 [85] "PER2--HDAC4"                "PFKFB3--B2M"                "PFKL--SUMO3"                "PLEC--ZC3H3"                "PPP1R12C--LENG8"            "PPP6R2--SAP25"             
 [91] "PPP6R2--SELENOO"            "PQLC1--NFATC1"              "PQLC1--ZADH2"               "PRDM16--SKI"                "PREX1--ZFAS1"               "PTMA--CXCR4"               
 [97] "PVT1--MYC"                  "RALGDS--LCNL1"              "RBBP8--HNRNPH1"             "REV3L--FYN"                 "RFX3--SFPQ"                 "RIMBP2--CHMP1A"            
[103] "RNF126--DAZAP1"             "SBNO2--C19orf24"            "SBNO2--DAZAP1"              "SBNO2--RNF126"              "SCFD2--FIP1L1"              "SCN8A--SCN8A"              
[109] "SENP3-EIF4A1--OAZ1"         "SENP3-EIF4A1--SAP25"        "SENP3-EIF4A1--UBB"          "SHANK3--BRD1"               "SLC16A3--METRNL"            "SPRED2--SERTAD2"           
[115] "SRGAP2B--SRGAP2B"           "SS18L1--TAF4"               "SUN1--PDGFA"                "TACC1--FGFR1"               "TAF3--TAF3"                 "TBC1D22A--BRD1"            
[121] "TCF25--ANKRD11"             "TCF25--SLC7A5"              "TCF25--TRABD"               "TET2--PPA2"                 "TFDP2--XRN1"                "TRPM2--SUMO3"              
[127] "TTYH3--ADAP1"               "TTYH3--C7orf50"             "TTYH3--FAM20C"              "TTYH3--MICALL2"             "TTYH3--SLC7A5"              "TUBGCP6--BRD1"             
[133] "UNKL--TMEM8A"               "UVSSA--GAK"                 "VPS37B--UBC"                "WNK1--NINJ2"                "YWHAE--UBC"                 "YWHAZ--KLF10"              
[139] "YWHAZ--MYC"                 "YWHAZ--ZNF706"              "ZC3H3--AGO2"                "ZEB2--ARHGAP15"             "ZFP36L2--PPM1B"           

Reproducibility Checklist

• The dependencies required to run the code in this pull request have been added to the project Dockerfile.
• This analysis has been added to continuous integration.

Documentation Checklist

• This analysis module has a README and it is up to date.
• This analysis is recorded in the table in analyses/README.md and the entry is up to date.
• The analytical code is documented and contains comments.

[jharenza]

@ewafula I ended up just removing "GTEx_Recurrent" altogether from the bash script artifact filter. There are diffs here, but I am going to chalk it up to this being run for subtyping with base histologies (v11) vs after subtyping (now) with histologies. I think we can just merge this for now.