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Untitled.R
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#Package data future
#Group_list default
Feature_lst_hg19 = list(
HNRNPC_eCLIP = eCLIP_HNRNPC_gr,
YTHDC1_TREW = YTHDC1_TREW_gr,
YTHDF1_TREW = YTHDF1_TREW_gr,
YTHDF2_TREW = YTHDF2_TREW_gr,
miR_targeted_genes = miR_targeted_genes_grl,
miRanda = miRanda_hg19_gr,
TargetScan = TargetScan_hg19_gr,
Verified_miRtargets = verified_targets_gr
)
group_list_default = list(
UTR5 = c("UTR5", "Pos_UTR5", "length_UTR5"),
CDS = c("CDS", "Pos_CDS", "length_CDS"),
UTR3 = c("UTR3", "Pos_UTR3", "length_UTR3"),
Exon = c("exons", "Pos_exons", "long_exon","Last_exons_50bp"),
Gene = c("Pos_Tx","length_gene_ex","length_gene_full","Isoform_num","sncRNA","lncRNA","HK_genes"),
LandMarks = c("m6Am","Start_codons","Stop_codons"),
Motif = c("AAACA","GAACA","AGACA","GGACA","AAACT","GAACT","AGACT","GGACT","AAACC","GAACC","AGACC","GGACC"),
Structure = c("struct_hybridize","struct_loop"),
Evolution = c("PC_1nt","PC_101nt","FC_1nt","FC_101nt"),
miRNA_RBP = c("HNRNPC_eCLIP", "YTHDC1_TREW", "YTHDF1_TREW", "YTHDF2_TREW", "miR_targeted_genes","TargetScan","Verified_miRtargets"),
Batch = c("GC_cont_genes","GC_cont_101bp","Intercept")
)
names(group_list_default) = c("5'UTR","CDS","3'UTR","Exon","Gene","Marks","Motif","Struc","Evolution","miRNA & RBP","Batch")
readRDS("")
readRDS("")
readRDS("")
setwd("/Users/zhenwei/Documents/GitHub/m6ALogisticModel")
eCLIP_HNRNPC_gr <- readRDS("/Users/zhenwei/Documents/GitHub/TREW-cons/I_GLM_feature_prep_2018_1_4/eCLIP_HNRNPC.rds")
devtools::use_data(eCLIP_HNRNPC_gr,overwrite = TRUE)
YTHDC1_TREW_gr <- readRDS("/Users/zhenwei/Documents/GitHub/TREW-cons/I_GLM_feature_prep_2018_1_4/YTHDC1_TREW_gr.rds")
devtools::use_data(YTHDC1_TREW_gr)
YTHDF1_TREW_gr <- readRDS("/Users/zhenwei/Documents/GitHub/TREW-cons/I_GLM_feature_prep_2018_1_4/YTHDF1_TREW_gr.rds")
devtools::use_data(YTHDF1_TREW_gr)
YTHDF2_TREW_gr <- readRDS("/Users/zhenwei/Documents/GitHub/TREW-cons/I_GLM_feature_prep_2018_1_4/YTHDF2_TREW_gr.rds")
devtools::use_data(YTHDF2_TREW_gr)
miR_targeted_genes_grl <- readRDS("/Users/zhenwei/Documents/GitHub/TREW-cons/I_GLM_feature_prep_2018_1_4/miR_targeted_genes_grl.rds")
devtools::use_data(miR_targeted_genes_grl)
TargetScan_hg19_gr <- readRDS("/Users/zhenwei/Documents/GitHub/TREW-cons/I_GLM_feature_prep_2018_1_4/TargetScan_hg19_gr.rds")
devtools::use_data(TargetScan_hg19_gr)
verified_targets_gr <- readRDS("/Users/zhenwei/Documents/GitHub/TREW-cons/I_GLM_feature_prep_2018_1_4/verified_targets.rds")
devtools::use_data(verified_targets_gr)
verified_targets_gr <- readRDS("/Users/zhenwei/Documents/GitHub/TREW-cons/I_GLM_feature_prep_2018_1_4/verified_targets.rds")
SE_Learning <- readRDS("/Users/zhenwei/Documents/GitHub/TREW-cons/J_GLM_Learning_2018_1_15/SE_Learning.rds")
mcols( SE_Learning ) = NULL
idx_1 <- assay(SE_Learning) == 1
idx_NA <- assay(SE_Learning) == 0
idx_n1 <- assay(SE_Learning) == -1
assay(SE_Learning)[idx_NA] = NA
assay(SE_Learning)[idx_n1] = 0
assay(SE_Learning)[idx_1] = 1
file.list <- grep("\\.",list.files("/Users/zhenwei/Documents/GitHub/TREW-cons/Targets_collection"),value = T, invert = T)
SE_Learning$ID = file.list
SE_example = SE_Learning
setwd("/Users/zhenwei/Documents/GitHub/m6ALogisticModel")
devtools::use_data(SE_example)
METTL16_CLIP <- readRDS("/Users/zhenwei/Documents/GitHub/TREW-cons/More\ Modeling\ triles/METTL16_CLIP.rds")
devtools::use_data(METTL16_CLIP)
ALKBH5_PARCLIP <- readRDS("/Users/zhenwei/Documents/GitHub/TREW-cons/More\ Modeling\ triles/PARCLIP_ALKBH5.rds")
devtools::use_data(ALKBH5_PARCLIP)
FTO_CLIP <- readRDS("/Users/zhenwei/Documents/GitHub/TREW-cons/More\ Modeling\ triles/CLIP_FTO.rds")
devtools::use_data(FTO_CLIP)
FTO_eCLIP <- readRDS("/Users/zhenwei/Documents/GitHub/TREW-cons/More\ Modeling\ triles/eCLIP_FTO.rds")
devtools::use_data(FTO_eCLIP)
METTL3_TREW <- readRDS("/Users/zhenwei/Documents/GitHub/TREW-cons/More\ Modeling\ triles/METTL3_TREW_gr.rds")
devtools::use_data(METTL3_TREW,overwrite = TRUE)
METTL14_TREW <- readRDS("/Users/zhenwei/Documents/GitHub/TREW-cons/More\ Modeling\ triles/METTL14_TREW_gr.rds")
devtools::use_data(METTL14_TREW,overwrite = TRUE)
WTAP_TREW <- readRDS("/Users/zhenwei/Documents/GitHub/TREW-cons/More\ Modeling\ triles/WTAP_TREW_gr.rds")
devtools::use_data(WTAP_TREW,overwrite = TRUE)
hg19_miCLIP_gr <- readRDS("/Users/zhenwei/Documents/GitHub/Project_X/hg19_miCLIP_ml.rds")
devtools::use_data(hg19_miCLIP_gr,overwrite = TRUE,pkg = "/Users/zhenwei/Documents/GitHub/m6ALogisticModel")
group_list_expanded = list(
UTR5 = c("UTR5", "Pos_UTR5", "length_UTR5"),
CDS = c("CDS", "Pos_CDS", "length_CDS"),
UTR3 = c("UTR3", "Pos_UTR3", "length_UTR3"),
Exon = c("exons", "Pos_exons", "long_exon","Last_exons_50bp"),
Gene = c("Pos_Tx","length_gene_ex","length_gene_full","Isoform_num","sncRNA","lncRNA","HK_genes"),
LandMarks = c("m6Am","Start_codons","Stop_codons"),
Motif = c("AAACA","GAACA","AGACA","GGACA","AAACT","GAACT","AGACT","GGACT","AAACC","GAACC","AGACC","GGACC"),
Structure = c("struct_hybridize","struct_loop"),
Evolution = c("PC_1nt","PC_101nt","FC_1nt","FC_101nt"),
miRNA_RBP = c("HNRNPC_eCLIP", "YTHDC1_TREW", "YTHDF1_TREW", "YTHDF2_TREW", "miR_targeted_genes","TargetScan","Verified_miRtargets"),
Writers_Erasers = c("METTL3_TREW","METTL14_TREW","WTAP_TREW","METTL16_CLIP","ALKBH5_PARCLIP","FTO_CLIP","FTO_eCLIP"),
Batch = c("GC_cont_genes","GC_cont_101bp","Intercept")
)
devtools::use_data(group_list_expanded)