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casbap / ncRNA

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GO table consistency #6

Closed markziemann closed 2 years ago

markziemann commented 2 years ago

Why is there so much inconsistency in the way GO table is referenced?

(base) mdz@ziemann-01:~/projects/ncRNA$ grep GO_table *Rmd
HumanImputationBlinded.Rmd:GO_table <-"GOtable.rds"
HumanImputationBlinded.Rmd:GO_table <- readRDS(GO_table)
HumanImputationBlinded.Rmd:# From GO_table, selected randomly as training data
HumanImputation.Rmd:GO_table <- "GO_table.rds"
HumanImputation.Rmd:GO_table <- readRDS(GO_table)
HumanImputation.Rmd:cluster1GO <- GO_table[GO_table$ensembl_gene_id %in% cluster1_list,]
HumanImputation.Rmd:nullOnt <- setdiff(unique(rownames(agg)),unique(GO_table$ensembl_gene_id))
(base) mdz@ziemann-01:~/projects/ncRNA$ grep GOtable.rds *Rmd
HumanGoPrep.Rmd:saveRDS(GOtable, "GOtable.rds")
HumanImputationBlinded.Rmd:GO_table <-"GOtable.rds"
(base) mdz@ziemann-01:~/projects/ncRNA$ grep GOtable *Rmd
HumanGoPrep.Rmd:GOtable <- orgGOmatrixwide
HumanGoPrep.Rmd:GOtable <- GOtable[-IndexRemoved,]
HumanGoPrep.Rmd:dim(GOtable)
HumanGoPrep.Rmd:head(rowSums(GOtable[,2:ncol(GOtable)]),50)
HumanGoPrep.Rmd:saveRDS(GOtable, "GOtable.rds")
HumanGoPrep.Rmd:test_size <- floor(0.10 * nrow(GOtable))
HumanGoPrep.Rmd:blinded_ind <- sample(seq_len(nrow(GOtable)), size = test_size)
HumanGoPrep.Rmd:GOtrain <- GOtable
HumanGoPrep.Rmd:GO_test <- GOtable[blinded_ind,]
HumanImputationBlinded.Rmd:GO_table <-"GOtable.rds"