Nothing
## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----metapred1----------------------------------------------------------------
library(driveR)
path2annovar_csv <- system.file("extdata/example.hg19_multianno.csv",
package = "driveR")
## ----metapred2----------------------------------------------------------------
metaprediction_df <- predict_coding_impact(annovar_csv_path = path2annovar_csv)
head(metaprediction_df)
## ----metapred3, eval=FALSE----------------------------------------------------
# metaprediction_df <- predict_coding_impact(annovar_csv_path = path2annovar_csv,
# keep_highest_score = FALSE)
## ----metapred4, eval=FALSE----------------------------------------------------
# metaprediction_df <- predict_coding_impact(annovar_csv_path = path2annovar_csv,
# keep_single_symbol = FALSE)
## ----metapred5, eval=FALSE----------------------------------------------------
# metaprediction_df <- predict_coding_impact(annovar_csv_path = path2annovar_csv,
# na.string = "NA")
## ----setup, eval=FALSE--------------------------------------------------------
# library(driveR)
## ----example_av_csv-----------------------------------------------------------
path2annovar_csv <- system.file("extdata/example.hg19_multianno.csv",
package = "driveR")
## ----example_scna-------------------------------------------------------------
head(example_scna_table)
## ----phenolyzer_input,eval=FALSE----------------------------------------------
# phenolyzer_genes <- create_features_df(annovar_csv_path = path2annovar_csv,
# scna_df = example_scna_table,
# prep_phenolyzer_input = TRUE,
# build = "GRCh37")
## ----save_phenolyzer_input, eval=FALSE----------------------------------------
# write.table(x = data.frame(gene = phenolyzer_genes),
# file = "input_genes.txt",
# row.names = FALSE, col.names = FALSE, quote = FALSE)
## ----example_phenoylzer-------------------------------------------------------
path2phenolyzer_out <- system.file("extdata/example.annotated_gene_list",
package = "driveR")
## ----features_df, eval=FALSE--------------------------------------------------
# features_df <- create_features_df(annovar_csv_path = path2annovar_csv,
# scna_df = example_scna_table,
# phenolyzer_annotated_gene_list_path = path2phenolyzer_out,
# build = "GRCh37")
## ----features_df_load, echo=FALSE---------------------------------------------
features_df <- example_features_table
## ----cancer_types-------------------------------------------------------------
knitr::kable(MTL_submodel_descriptions)
## ----driver_prob--------------------------------------------------------------
driver_prob_df <- prioritize_driver_genes(features_df = features_df,
cancer_type = "LUAD")
head(driver_prob_df, 10)
## ----setup2, eval = FALSE-----------------------------------------------------
# library(driveR)
## ----example_av_csv2----------------------------------------------------------
path2annovar_csv <- system.file("extdata/example_cohort.hg19_multianno.csv",
package = "driveR")
## ----example_scna2------------------------------------------------------------
head(example_cohort_scna_table)
## ----phenolyzer_input2, eval=FALSE--------------------------------------------
# phenolyzer_genes <- create_features_df(annovar_csv_path = path2annovar_csv,
# scna_df = example_cohort_scna_table,
# prep_phenolyzer_input = TRUE,
# batch_analysis = TRUE)
## ----save_phenolyzer_input2, eval=FALSE---------------------------------------
# write.table(x = data.frame(gene = phenolyzer_genes),
# file = "input_genes.txt",
# row.names = FALSE, col.names = FALSE, quote = FALSE)
## ----example_phenoylzer2------------------------------------------------------
path2phenolyzer_out <- system.file("extdata/example_cohort.annotated_gene_list",
package = "driveR")
## ----features_df2, eval=FALSE-------------------------------------------------
# features_df <- create_features_df(annovar_csv_path = path2annovar_csv,
# scna_df = example_cohort_scna_table,
# phenolyzer_annotated_gene_list_path = path2phenolyzer_out,
# batch_analysis = TRUE)
## ----features_df_load2, echo=FALSE--------------------------------------------
features_df <- example_cohort_features_table
## ----driver_prob2-------------------------------------------------------------
driver_prob_df <- prioritize_driver_genes(features_df = features_df,
cancer_type = "LAML")
head(driver_prob_df, 10)
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