Description Usage Format Details Note
Defined by the following Code:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 | library(SummarizedExperiment)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(BSgenome.Hsapiens.UCSC.hg19)
library(fitCons.UCSC.hg19)
library(phastCons100way.UCSC.hg19)
Feature_List_expanded_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,
TargetScan = TargetScan_hg19_gr,
Verified_miRtargets = verified_targets_gr,
METTL3_TREW = METTL3_TREW,
METTL14_TREW = METTL14_TREW,
WTAP_TREW = WTAP_TREW,
METTL16_CLIP = METTL16_CLIP,
ALKBH5_PARCLIP = ALKBH5_PARCLIP,
FTO_CLIP = FTO_CLIP,
FTO_eCLIP = FTO_eCLIP
)
SE_features_added <- predictors.annot(se = SE_example,
txdb = TxDb.Hsapiens.UCSC.hg19.knownGene,
bsgnm = Hsapiens,
fc = fitCons.UCSC.hg19,
pc = phastCons100way.UCSC.hg19,
struct_hybridize = Struc_hg19,
feature_lst = Feature_List_expanded_hg19,
HK_genes_list = HK_hg19_eids)
logistic.modeling(
SE_features_added,
MCMC_iterations = 100000,
decision_method = "BPM",
save_dir = "LogisticModel_X",
sample_names_coldata = "ID",
group_list = group_list_expanded
)
|
A List object.
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") )
The list include an extra module called Writers_Erasers compared with \Codegroup_list_default, these data are published CLIP datasets of m6A writers and erasers.
For other provided list for grouping, please check group_list_default
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