add files

Fig2.md

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+---
+title: "Buteyn et al. Figure 2"
+author: "Tim Triche and Zach DeBruine"
+date: "2023-05-19"
+output:
+  html_document:
+    fig_width: 8
+    code_folding: hide
+    highlight: tango
+    toc: yes
+    keep_md: true
+    toc_float:
+      collapsed: yes
+---
+
+
+
+
+
+## Objective
+
+To map the transcriptional signatures of immune-cold transplant-refractory AML.
+
+In particular, to find out why FUS::ERG-driven AML is consistently immune-cold,
+to determine if specific biological processes are shared across transplant-
+refractory AML cases, and to see if this outcome can be predicted at diagnosis.
+
+
+## Approach
+
+### Steps 
+
+Using the previously fitted rank-90 non-negative matrix factorization model, 
+
+1. Identify factors describing specific signatures for cytogenetic subtypes.
+
+2. Investigate biological processes underlying these factors using GSEA.
+
+3. Determine if these factors are predictive of transplant-refractory AML.
+
+
+## Analysis
+
+We begin by loading the previously fitted NMF model (refer to TARGET_NMF.Rmd). 
+
+
+```
+## [1]   90 1630
+```
+
+Next we load the original annotated RNAseq data and check that everyone's there.
+
+
+```
+## [1] FALSE
+```
+
+### Slight hiccup 
+
+Unfortunately we are missing some of the rarer fusions! We can fix that, though.
+In the process we will recover a few others that slipped through earlier on. 
+When we just need to update a model with some new observations, we can use the
+singlet::ProjectData() function with our existing W matrix.
+
+![plot of chunk unnamed-chunk-3](figure/unnamed-chunk-3-1.png)
+
+Let's take a quick look at a UMAP of (projected) dx NMF versus the original NMF.
+
+![plot of chunk unnamed-chunk-4](figure/unnamed-chunk-4-1.png)
+
+It's not exactly identical to Zach's, but the FUS-ERG cases do split off. 
+That's good enough for the time being. Let's add in the other fusions now.
+
+
+```
+## Error in file(file, "rt"): cannot open the connection
+```
+
+```
+## Error in eval(expr, envir, enclos): object 'target_covs' not found
+```
+
+```
+## [1] 1682
+```
+
+```
+## [1] 1682
+```
+
+
+
+|fusion        | Freq|
+|:-------------|----:|
+|KMT2A-MLLT11  |    7|
+|NPM1-MLF1     |    8|
+|HNRNPH1-ERG   |    9|
+|RBM15-MKL1    |   13|
+|RUNX1-CBFA2T3 |   13|
+|FUS-ERG       |   14|
+|KAT6A-CREBBP  |   14|
+|KMT2A-SEPT6   |   14|
+|ETV6-MNX1     |   16|
+|KMT2A-MLLT1   |   21|
+|ETV6-X        |   25|
+|NUP98-KDM5A   |   38|
+|CBFA2T3-GLIS2 |   42|
+|KMT2A-ELL     |   49|
+|KMT2A-MLLT4   |   49|
+|DEK-NUP214    |   55|
+|KMT2A-MLLT10  |   92|
+|KMT2A-MLLT3   |  126|
+|NUP98-NSD1    |  137|
+|CBFB-MYH11    |  186|
+|RUNX1-RUNX1T1 |  218|
+|None          |  536|
+
+
+Let's feed the additional fusions, projected onto the original NMF, to the 
+original UMAP model. 
+
+
+
+We can fit factors to fusions:
+
+
+```
+## [1] "85"
+```
+
+```
+## [1] 85
+```
+
+```
+## STAB1 
+##   261
+```
+
+```
+## [1] "65" "73" "21" "48" "27"
+```
+
+```
+## [1] 65
+```
+
+```
+## CCND2 
+##  4860
+```
+
+```
+## character(0)
+```
+
+```
+## [1] "76"
+```
+
+```
+## TP53INP1 
+##    11479
+```
+
+```
+## [1] "21" "2"
+```
+
+```
+## BAHCC1 
+##  47621
+```
+
+```
+## MALAT1 
+##  39004
+```
+
+We can also fit some more interesting outcomes, albeit only for exploration:
+
+
+```
+##  [1] "16" "40" "87" "82" "45" "2"  "44" "46" "1"  "39" "48" "8"  "4"  "55" "90"
+## [16] "15" "14" "5"  "68" "52" "7"  "12" "81" "9"  "78" "53" "89" "42" "11" "77"
+## [31] "43" "31" "20" "3"  "10" "26" "6"  "80" "60" "29" "35" "34" "50" "18" "30"
+## [46] "13" "47" "32" "86" "71" "33" "72" "17" "21" "28" "88" "36" "63" "22" "25"
+## [61] "23" "61" "38" "62" "58" "19" "24" "41" "37" "69" "49" "27" "66" "54" "51"
+## [76] "56" "57" "59" "83" "64" "70" "75" "67" "74" "76" "73" "79" "65" "85"
+```
+
+```
+##  [1] "40" "87" "16" "82" "44" "2"  "45" "39" "52" "68" "15" "8"  "46" "1"  "14"
+## [16] "4"  "48" "55" "5"  "90" "21" "81" "37" "9"  "7"  "31" "77" "89" "12" "78"
+## [31] "53" "3"  "42" "20" "10" "43" "26" "6"  "30" "29" "80" "35" "51" "28" "18"
+## [46] "34" "50" "33" "60" "13" "58" "86" "11" "72" "71" "47" "62" "23" "36" "66"
+## [61] "41" "83" "38" "88" "49" "27" "32" "70" "22" "69"
+```
+
+We can also quickly check things out with iSEE:
+
+
+Well, that looks good. 
+
+
+### Figure panels: 
+
+A. UMAP of TARGET pAML (n = 1682) samples colored by cytogenetic subtype.
+
+![plot of chunk unnamed-chunk-10](figure/unnamed-chunk-10-1.png)
+
+B. Association of individual factors with FUS::ERG vs. all other pAML. 
+
+C. Enrichnment of factors in cytogenetic subtypes of pediatric AML.
+
+D. Pathway enrichment for factors associated with allo-SCT response.
+
+E. Antigen presentation and immune response GSEA, FUS::ERG vs. other pAML.
+

fusions.txt

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+CBFA2T3-GLIS2	
+CBFB-MYH11	
+DEK-NUP214	
+ETV6-X
+ETV6-MNX1	
+FUS-ERG	
+KAT6A-CREBBP	
+KMT2A-ELL	
+KMT2A-MLLT1	
+KMT2A-MLLT10	
+KMT2A-MLLT11	
+KMT2A-MLLT3	
+KMT2A-MLLT4	
+KMT2A-SEPT6	
+None	
+NPM1-MLF1	
+NUP98-KDM5A	
+NUP98-NSD1	
+RBM15-MKL1	
+RUNX1-CBFA2T3	
+RUNX1-RUNX1T1
+HNRNPH1-ERG