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removed local rearrangement filter for onco (#567)
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Co-authored-by: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
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@kgaonkar6 @jaclyn-taroni
kgaonkar6 and jaclyn-taroni authored Mar 6, 2020
1 parent 516201f commit cdcd377
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Showing 7 changed files with 24,401 additions and 23,621 deletions.
22 changes: 13 additions & 9 deletions analyses/fusion_filtering/04-project-specific-filtering.Rmd
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Expand Up @@ -12,11 +12,11 @@ params:
input: string
dataStranded:
label: "Input filtered fusion dataframe"
value: scratch/standardFusionStrandedExp_QC_expression_filtered_annotated.RDS
value: scratch/standardFusionStrandedExp_QC_expression_GTExComparison_annotated.RDS
input: file
dataPolya:
label: "Input filtered fusion dataframe"
value: scratch/standardFusionPolyaExp_QC_expression_filtered_annotated.RDS
value: scratch/standardFusionPolyaExp_QC_expression_GTExComparison_annotated.RDS
input: file
numCaller:
label: "Least Number of callers to have called fusion"
Expand Down Expand Up @@ -117,22 +117,18 @@ fusion_caller.summary <- fusion_calls %>%
dplyr::mutate(CalledBy = toString(Caller), caller.count = n()) %>%
dplyr::select(-Caller)
# remove fusion within local rearrangement
fusion_calls <- fusion_calls %>%
# remove local rearrangement/adjacent genes
dplyr::filter(!grepl("LOCAL_REARRANGEMENT|LOCAL_INVERSION",annots))
#to add aggregated caller from fusion_caller.summary
fusion_calls<-fusion_calls %>%
dplyr::select(-Caller,-annots) %>%
left_join(fusion_caller.summary,by=(c("Sample","FusionName","Fusion_Type"))) %>%
dplyr::select(-JunctionReadCount,-SpanningFragCount,-Confidence,-LeftBreakpoint,-RightBreakpoint) %>% unique()
#merge with histology file
fusion_calls<-merge(fusion_calls,clinical,by.x="Sample",by.y="Kids_First_Biospecimen_ID")
# filter for putative driver genes and mutifused genes per sample
# filter for putative driver genes
putative_driver_annotated_fusions <- fusion_calls %>%
dplyr::select(-Caller,-annots) %>%
unique() %>%
dplyr::filter(!is.na(Gene1A_anno) | !is.na(Gene1B_anno) | !is.na(Gene2A_anno) | !is.na(Gene2B_anno)) %>%
unique()
Expand All @@ -143,6 +139,14 @@ putative_driver_annotated_fusions <- fusion_calls %>%


```{r}
# remove local rearrangements
fusion_calls<-fusion_calls %>%
# remove local rearrangement/adjacent genes
dplyr::filter(!grepl("LOCAL_REARRANGEMENT|LOCAL_INVERSION",annots)) %>%
dplyr::select(-Caller,-annots) %>%
unique()
# Gene fusion should be in-frame/frameshift
fusion_calls<-fusion_calls %>%
dplyr::filter(Fusion_Type != "other")
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522 changes: 522 additions & 0 deletions analyses/fusion_filtering/04-project-specific-filtering.nb.html
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36,708 changes: 18,354 additions & 18,354 deletions analyses/fusion_filtering/results/FilteredFusion.tsv
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8,961 changes: 4,607 additions & 4,354 deletions analyses/fusion_filtering/results/pbta-fusion-putative-oncogenic.tsv
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14 changes: 7 additions & 7 deletions analyses/fusion_filtering/results/pbta-fusion-recurrent-fusion-bysample.tsv
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Expand Up @@ -72,6 +72,7 @@ BS_2ADZNNV4 0 0 1 0 0
BS_2AR3AP0N 0 0 0 1 0
BS_2EMW8ZG3 0 0 0 1 0
BS_2EN3X6HB 0 0 0 1 0
BS_2HN96129 0 0 0 1 0
BS_2JP7RBMB 0 0 0 1 0
BS_2KJ2YAZR 0 0 0 1 0
BS_2R9TCR03 0 0 0 1 0
Expand Down Expand Up @@ -167,6 +168,7 @@ BS_5CTVXVRX 0 0 0 1 0
BS_5JM573JC 0 0 0 1 0
BS_5K3R0F5D 0 0 0 1 0
BS_5NWDARXG 0 0 0 1 0
BS_5P1TN10Z 0 0 0 1 0
BS_5P3CZQV8 0 0 0 1 0
BS_5PEFNDCY 0 0 1 0 0
BS_5PJCHF6V 0 0 0 1 0
Expand Down Expand Up @@ -200,6 +202,7 @@ BS_6NTXGQAC 0 0 0 1 0
BS_6R7SFVV2 0 0 0 1 0
BS_6T4JGBGY 0 0 0 1 0
BS_6VF6VPCG 0 0 0 1 0
BS_6VPKXXMR 0 0 0 1 0
BS_6WP1FHTE 0 0 0 1 0
BS_6YMJ621P 0 0 0 1 0
BS_70FFPA51 0 0 0 1 0
Expand All @@ -225,13 +228,13 @@ BS_7WM3MNZ0 0 0 0 1 0
BS_7XQRH69M 0 0 0 1 0
BS_7XRN3CFX 0 0 0 1 0
BS_7Z93ZYMS 0 0 1 0 0
BS_7ZV3DPGT 0 0 0 1 0
BS_81SP2HX4 0 0 0 1 0
BS_84XCR9GG 0 0 0 1 0
BS_850BAHH9 0 0 0 1 0
BS_86Q14TZG 0 0 0 1 0
BS_8D0NYM46 0 0 0 1 0
BS_8F9BDWY4 0 0 0 1 0
BS_8GW1TMV2 0 0 0 1 0
BS_8J09S6MZ 0 0 0 1 0
BS_8J3B6ZB6 0 0 1 0 0
BS_8NY9J9NQ 0 0 0 1 0
Expand Down Expand Up @@ -554,8 +557,8 @@ BS_M1T1K5WV 0 0 0 1 0
BS_M4923M40 0 0 0 1 0
BS_M4NVX721 0 0 0 1 0
BS_M4TTKPNR 0 0 1 0 0
BS_M7QJ8VF0 0 0 0 1 0
BS_M84H3KXA 0 0 0 1 0
BS_M85CXHDV 0 0 0 1 0
BS_M86ECPHK 0 0 0 1 0
BS_M8M56Z4Y 0 0 1 0 0
BS_M8WP5T16 0 0 0 1 0
Expand All @@ -573,6 +576,7 @@ BS_MGAMKKBD 0 0 0 1 0
BS_MKM0EEN1 0 0 0 1 0
BS_MM20BVW9 0 0 0 1 0
BS_MMNRZ1EQ 0 0 0 1 0
BS_MN5XVP5A 0 0 0 1 0
BS_MQCKXD60 0 0 0 1 0
BS_MT15SGJN 1 0 0 0 0
BS_MVW01FPB 0 0 0 1 0
Expand Down Expand Up @@ -647,6 +651,7 @@ BS_QB7YGKN1 0 0 0 1 0
BS_QB84TBA3 0 0 0 1 0
BS_QBR4WCQ2 0 0 0 1 0
BS_QC3XCE6X 0 0 0 1 0
BS_QEYPFYHD 0 0 0 1 0
BS_QF5VVZX5 0 0 0 1 0
BS_QH82PBMB 0 0 1 0 0
BS_QKT3TJVK 0 0 0 1 0
Expand All @@ -673,16 +678,13 @@ BS_R7NTZR4C 0 0 0 1 0
BS_R9B92M75 0 0 0 1 0
BS_RB2S0KDF 0 0 0 1 0
BS_RCC8BXVE 0 0 0 1 0
BS_RCCN63K6 0 0 0 1 0
BS_RCFQ31XF 0 0 0 1 0
BS_RD4D5F9F 0 0 0 1 0
BS_RFMQ7T0T 0 0 0 1 0
BS_RGPSEMHC 0 0 0 1 0
BS_RGSMX7QD 0 0 1 0 0
BS_RHD7XPNP 0 0 0 1 0
BS_RR12T74P 0 0 0 1 0
BS_RRAEQZ97 0 0 0 1 0
BS_RSRPX3S8 0 0 0 1 0
BS_RVSEDNJ4 0 0 1 0 0
BS_RWJZFTP9 0 0 1 0 0
BS_RX1YTZ7F 0 0 0 0 1
Expand Down Expand Up @@ -739,7 +741,6 @@ BS_TMTV769C 0 0 0 1 0
BS_TNRHHYNC 0 0 0 1 0
BS_TQ5QHR17 0 0 0 1 0
BS_TRKH2SPE 0 0 0 1 0
BS_TV5B86ZD 0 0 0 1 0
BS_TW8DQH8J 0 0 0 1 0
BS_TXY8QYWA 0 0 0 1 0
BS_TXZ7KHTQ 0 0 0 1 0
Expand Down Expand Up @@ -868,7 +869,6 @@ BS_Z6BWR941 0 0 1 0 0
BS_Z6MC4N8D 0 0 0 1 0
BS_Z72QAZC7 0 0 0 1 0
BS_Z7G68ZS2 0 0 0 1 0
BS_Z7PKVY9J 0 0 0 1 0
BS_Z7Y2466H 0 0 1 0 0
BS_Z85M2R3N 0 0 0 1 0
BS_Z8F3GM85 0 0 0 1 0
Expand Down
3 changes: 2 additions & 1 deletion analyses/fusion_filtering/results/pbta-fusion-recurrently-fused-genes-byhistology.tsv
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Expand Up @@ -4,7 +4,7 @@ KIAA1549 Low-grade astrocytic tumor 109
C11orf95 Ependymal tumor 28
RELA Ependymal tumor 25
BRAF Neuronal and mixed neuronal-glial tumor 8
MET Diffuse astrocytic and oligodendroglial tumor 7
MET Diffuse astrocytic and oligodendroglial tumor 8
KIAA1549 Neuronal and mixed neuronal-glial tumor 6
EWSR1 Mesenchymal non-meningothelial tumor 5
FLI1 Mesenchymal non-meningothelial tumor 5
Expand All @@ -13,3 +13,4 @@ REV3L Diffuse astrocytic and oligodendroglial tumor 5
NTRK2 Low-grade astrocytic tumor 4
RAF1 Low-grade astrocytic tumor 4
ROS1 Low-grade astrocytic tumor 4
SCFD2 Diffuse astrocytic and oligodendroglial tumor 4
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