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Fix issue in the Transcript Pass logic that would cause pVACview to crash on retiering #1459

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Fix issue in the Transcript Pass logic that would cause pVACview to crash on retiering #1459

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15 changes: 1 addition & 14 deletions pvactools/tools/pvacview/input_processing_functions.R
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Original file line number Diff line number Diff line change
Expand Up @@ -91,20 +91,7 @@ set_formatting_columns <- function(df) {
df$mainTable$`RNA VAF Fail` <- apply(df$mainTable, 1, function(x) {!is.na(x['RNA VAF']) && as.numeric(x['RNA VAF']) <= as.numeric(df$metricsData['trna_vaf'])})
df$mainTable$`RNA Depth Fail` <- apply(df$mainTable, 1, function(x) {!is.na(x['RNA Depth']) && as.numeric(x['RNA Depth']) <= as.numeric(df$metricsData['trna_cov'])})
df$mainTable$`Prob Pos Pass` <- apply(df$mainTable, 1, function(x) {is_probaa_pass(x["Prob Pos"])})
transcript_pass <- apply(df$mainTable, 1, function(x) {
if ('tsl' %in% df$transcript_prioritization_strategy && is_tsl_pass(x["TSL"], as.numeric(df$maximum_transcript_support_level))) {
return("True")
}
else if ('mane_select' %in% df$transcript_prioritization_strategy && is_mane_select_pass(x["MANE Select"])) {
return("True")
}
else if ('canonical' %in% df$transcript_prioritization_strategy && is_canonical_pass(x["Canonical"])) {
return("True")
}
else {
return("False")
}
})
transcript_pass <- apply(df$mainTable, 1, function(x) { ifelse(is_transcript_pass(x["Canonical"], x["MANE Select"], x["TSL"], df$transcript_prioritization_strategy, df$maximum_transcript_support_level), "True", "False") })
df$mainTable <- add_column(df$mainTable, `Transcript Pass` = transcript_pass, .after = "TSL")
return (df)
}
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28 changes: 2 additions & 26 deletions pvactools/tools/pvacview/server.R
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Expand Up @@ -348,19 +348,7 @@ server <- shinyServer(function(input, output, session) {
df$mainTable$`RNA VAF Fail` <- apply(df$mainTable, 1, function(x) {!is.na(x['RNA VAF']) && as.numeric(x['RNA VAF']) <= as.numeric(df$metricsData['trna_vaf'])})
df$mainTable$`RNA Depth Fail` <- apply(df$mainTable, 1, function(x) {!is.na(x['RNA Depth']) && as.numeric(x['RNA Depth']) <= as.numeric(df$metricsData['trna_cov'])})
df$mainTable$`Prob Pos Pass` <- apply(df$mainTable, 1, function(x) {is_probaa_pass(x["Prob Pos"])})
transcript_pass <- apply(df$mainTable, TRUE, function(x) {
if ('tsl' %in% df$transcript_prioritization_strategy && is_tsl_pass(x["TSL"], as.numeric(df$maximum_transcript_support_level))) {
return("True")
}
if ('mane_select' %in% df$transcript_prioritization_strategy && is_mane_select_pass(x["MANE Select"])) {
return("True")
}
if ('canonical' %in% df$transcript_prioritization_strategy && is_canonical_pass(x["Canonical"])) {
return("True")
}
return("False")
})
df$mainTable <- add_column(df$mainTable, `Transcript Pass` = transcript_pass, .after = "TSL")
df$mainTable$`Transcript Pass` <- apply(df$mainTable, 1, function(x) { ifelse(is_transcript_pass(x["Canonical"], x["MANE Select"], x["TSL"], df$transcript_prioritization_strategy, df$maximum_transcript_support_level), "True", "False") })
tier_sorter <- c("Pass", "PoorBinder", "PoorImmunogenicity", "PoorPresentation", "RefMatch", "PoorTranscript", "LowExpr", "Anchor", "Subclonal", "ProbPos", "Poor", "NoExpr")
df$mainTable$`Rank` <- rank(desc(as.numeric(replace(df$mainTable$`Allele Expr`, is.na(df$mainTable$`Allele Expr`), 0))), ties.method = "first")
for (metric in df$scoring_candidate_metric) {
Expand Down Expand Up @@ -420,19 +408,7 @@ server <- shinyServer(function(input, output, session) {
df$mainTable$`RNA VAF Fail` <- apply(df$mainTable, 1, function(x) {!is.na(x['RNA VAF']) && as.numeric(x['RNA VAF']) <= as.numeric(df$metricsData['trna_vaf'])})
df$mainTable$`RNA Depth Fail` <- apply(df$mainTable, 1, function(x) {!is.na(x['RNA Depth']) && as.numeric(x['RNA Depth']) <= as.numeric(df$metricsData['trna_cov'])})
df$mainTable$`Prob Pos Pass` <- apply(df$mainTable, 1, function(x) {is_probaa_pass(x["Prob Pos"])})
transcript_pass <- apply(df$mainTable, TRUE, function(x) {
if ('tsl' %in% df$transcript_prioritization_strategy && is_tsl_pass(x["TSL"], as.numeric(df$maximum_transcript_support_level))) {
return("True")
}
if ('mane_select' %in% df$transcript_prioritization_strategy && is_mane_select_pass(x["MANE Select"])) {
return("True")
}
if ('canonical' %in% df$transcript_prioritization_strategy && is_canonical_pass(x["Canonical"])) {
return("True")
}
return("False")
})
df$mainTable <- add_column(df$mainTable, `Transcript Pass` = transcript_pass, .after = "TSL")
df$mainTable$`Transcript Pass` <- apply(df$mainTable, 1, function(x) { ifelse(is_transcript_pass(x["Canonical"], x["MANE Select"], x["TSL"], df$transcript_prioritization_strategy, df$maximum_transcript_support_level), "True", "False") })
tier_sorter <- c("Pass", "PoorBinder", "PoorImmunogenicity", "PoorPresentation", "RefMatch", "PoorTranscript", "LowExpr", "Anchor", "Subclonal", "ProbPos", "Poor", "NoExpr")
df$mainTable$`Rank` <- rank(desc(as.numeric(replace(df$mainTable$`Allele Expr`, is.na(df$mainTable$`Allele Expr`), 0))), ties.method = "first")
for (metric in df$scoring_candidate_metric) {
Expand Down
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