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JunyueC / sci-fate_analysis

Downstream analysis script for sci-fate (TF-gene linkage analysis / cell linkage analysis)
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could not find function "combine_exon_intron" #4

Open pigraul opened 4 years ago

pigraul commented 4 years ago

Hello,

Error happend when I ran the script Main_script_generate_full_new_cds_file.R. command:

result = sciRNAseq_gene_count_summary(report_folder)

screen output: Error in combine_exon_intron(df_gene, gene_count) : could not find function "combine_exon_intron"

In which script or R package can I get the function "combine_exon_intron" ?

Thanks, raulee

JunyueC commented 4 years ago

Dear Raulee,

Sorry for missing this function. Attached please see the script and let me know if there are any questions.

combine_exon_intron <- function(df_gene, gene_count) { gene_count_exon = gene_count[df_gene$exon_intron == "exon", ] gene_count_intron = gene_count[df_gene$exon_intron == "intron", ] if(nrow(gene_count_exon) == nrow(gene_count_intron)) { gene_count_combine = gene_count_exon + gene_count_intron } else { gene_count_combine = gene_count_exon[-nrow(gene_count_exon), ] + gene_count_intron gene_count_combine = rbind(gene_count_combine, gene_count_exon[nrow(gene_count_exon), ]) }

return(gene_count_combine)

}

On Aug 3, 2020, at 3:32 AM, raulee notifications@github.com wrote:

Hello,

Error happend when I ran the script Main_script_generate_full_new_cds_file.R. command:

result = sciRNAseq_gene_count_summary(report_folder)

screen output: Error in combine_exon_intron(df_gene, gene_count) : could not find function "combine_exon_intron"

In which script or R package can I get the function "combine_exon_intron" ?

Thanks, raulee

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pigraul commented 4 years ago

Thanks you ! @JunyueC

I have another question about the data in the script Main_script_TF_gene_linkage.R

define the location of chip-seq peak matrix downloaded from https://amp.pharm.mssm.edu/Harmonizome/dataset/ENCODE+Transcription+Factor+Targets

df_gene_TF_link_ENCODE = "./data/df_TF_gene_ENCODE.RData"

I wonder the data "df_TF_gene_ENCODE.RData" is suitable for mouse data?

Thanks, Raulee