create_report script template.Rmd

[junwoo2]

Lines 239 and 241

final[is.na(final$HGVSp_Short) & nchar(final$Reference_Allele)>5,"VarName"] <- paste0(final$Hugo_Symbol, " ", final$Chromosome, ":", final$Start_Position, " ", substr(final$Reference_Allele,1,3),"..", ">", final$Tumor_Seq_Allele2)[is.na(final$HGVSp_Short) & nchar(final$Reference_Allele)>5 ]

final[is.na(final$HGVSp_Short) & nchar(final$Tumor_Seq_Allele2)>5,"VarName"] <- paste0(final$Hugo_Symbol, " ", final$Chromosome, ":", final$Start_Position, " ", final$Reference_Allele,1,3, ">", substr(final$Tumor_Seq_Allele2,1,3),"..")[is.na(final$HGVSp_Short) & nchar(final$Tumor_Seq_Allele2)>5]

[rhshah]

@murphycj2 can you check this

[murphycj2]

will do!