Chapter 10 RIF Analysis
One of the additional steps in the pipeline is to calculate Regulatory Impact Factor (RIF) scores for either transcription factors (TF) or any gene of interest.
Genes that are not DE may still have a regulatory role that can be inferred from these abstract calculations. See https://doi.org/10.1093/bioinformatics/btq051
By setting the TFs = NA and all_genes_as_TF = TRUE we are telling the function to use all genes as possible TF. Otherwise, we could set all_genes_as_TF = FALSE and then manually provide a list of TFs. For example, one might download the list of TF off the animalTFDB (http://bioinfo.life.hust.edu.cn/AnimalTFDB/) to focus on.
DE_dataframes_list <-
DE_out %>%
purrr::map("DE_sig_PIF_df")
vst_norm_data <- GET_normalised_data(full_norm, vst_or_log2 = "VST")[[1]]
RIF_output <-
calculate_RIF(DE_output = DE_out,
TFs = NA,
norm_exp_data = vst_norm_data,
gene_annotations = gene_annot,
all_genes_as_TF = TRUE,
colData = SummarizedExperiment::colData(seq_data) ,
results_contrast_factor = Treatment,
samples_colname = sample_names)
##
##
## ******************* Start of - ARC *******************
##
## ARC - LR vs MAL
## Number of target genes: 8
## Number of TFs (or genes as TFS): 22258
## names of condition 1: ARC_004__LR, ARC_022__LR, ARC_032__LR, ARC_079__LR, ARC_149__LR
## names of condition 2: ARC_008__MAL, ARC_066__MAL, ARC_088__MAL, ARC_096__MAL, ARC_186__MAL
## Number of excluded genes (within condition SD == 0): 1658
## Registered S3 method overwritten by 'GGally':
## method from
## +.gg ggplot2
##
## Registered S3 method overwritten by 'ggnetwork':
## method from
## fortify.igraph ggtree
## Running RIF...
## Running RIF... COMPLETE
##
## ARC - LR vs LAL
## Number of target genes: 124
## Number of TFs (or genes as TFS): 22258
## names of condition 1: ARC_004__LR, ARC_022__LR, ARC_032__LR, ARC_079__LR, ARC_149__LR
## names of condition 2: ARC_052__LAL, ARC_112__LAL, ARC_136__LAL, ARC_184__LAL, ARC_193__LAL
## Number of excluded genes (within condition SD == 0): 1625
## Running RIF...
## Running RIF... COMPLETE
##
## ARC - MAL vs LAL
## Number of target genes: 179
## Number of TFs (or genes as TFS): 22258
## names of condition 1: ARC_008__MAL, ARC_066__MAL, ARC_088__MAL, ARC_096__MAL, ARC_186__MAL
## names of condition 2: ARC_052__LAL, ARC_112__LAL, ARC_136__LAL, ARC_184__LAL, ARC_193__LAL
## Number of excluded genes (within condition SD == 0): 1642
## Running RIF...
## Running RIF... COMPLETE
##
##
## ******************* End of - ARC *******************
##
##
## ******************* Start of - LHA *******************
##
## LHA - LR vs MAL
## Number of target genes: 4
## Number of TFs (or genes as TFS): 22258
## names of condition 1: LHA_004__LR, LHA_022__LR, LHA_032__LR, LHA_079__LR, LHA_149__LR
## names of condition 2: LHA_008__MAL, LHA_066__MAL, LHA_088__MAL, LHA_096__MAL, LHA_186__MAL
## Number of excluded genes (within condition SD == 0): 2600
## Running RIF...
## Running RIF... COMPLETE
##
## LHA - LR vs LAL
## Did not run RIF -- Number of target genes: 0
##
## LHA - MAL vs LAL
## Number of target genes: 2
## Number of TFs (or genes as TFS): 22258
## names of condition 1: LHA_008__MAL, LHA_066__MAL, LHA_088__MAL, LHA_096__MAL, LHA_186__MAL
## names of condition 2: LHA_052__LAL, LHA_112__LAL, LHA_136__LAL, LHA_184__LAL, LHA_193__LAL
## Number of excluded genes (within condition SD == 0): 2623
## Running RIF...
## Running RIF... COMPLETE
##
##
## ******************* End of - LHA *******************
##
##
## ******************* Start of - VMH *******************
##
## VMH - LR vs MAL
## Did not run RIF -- Number of target genes: 1
##
## VMH - LR vs LAL
## Number of target genes: 11
## Number of TFs (or genes as TFS): 22258
## names of condition 1: VMH_004__LR, VMH_022__LR, VMH_032__LR, VMH_079__LR, VMH_149__LR
## names of condition 2: VMH_052__LAL, VMH_112__LAL, VMH_136__LAL, VMH_184__LAL, VMH_193__LAL
## Number of excluded genes (within condition SD == 0): 2156
## Running RIF...
## Running RIF... COMPLETE
##
## VMH - MAL vs LAL
## Number of target genes: 5
## Number of TFs (or genes as TFS): 22258
## names of condition 1: VMH_008__MAL, VMH_066__MAL, VMH_088__MAL, VMH_096__MAL, VMH_186__MAL
## names of condition 2: VMH_052__LAL, VMH_112__LAL, VMH_136__LAL, VMH_184__LAL, VMH_193__LAL
## Number of excluded genes (within condition SD == 0): 2188
## Running RIF...
## Running RIF... COMPLETE
##
##
## ******************* End of - VMH *******************
##
##
## ******************* Start of - ABO *******************
##
## ABO - LR vs MAL
## Number of target genes: 2
## Number of TFs (or genes as TFS): 22258
## names of condition 1: ABO_004__LR, ABO_022__LR, ABO_032__LR, ABO_079__LR, ABO_149__LR
## names of condition 2: ABO_008__MAL, ABO_066__MAL, ABO_088__MAL, ABO_096__MAL, ABO_186__MAL
## Number of excluded genes (within condition SD == 0): 3352
## Running RIF...
## Running RIF... COMPLETE
##
## ABO - LR vs LAL
## Number of target genes: 19
## Number of TFs (or genes as TFS): 22258
## names of condition 1: ABO_004__LR, ABO_022__LR, ABO_032__LR, ABO_079__LR, ABO_149__LR
## names of condition 2: ABO_052__LAL, ABO_112__LAL, ABO_136__LAL, ABO_184__LAL, ABO_193__LAL
## Number of excluded genes (within condition SD == 0): 3206
## Running RIF...
## Running RIF... COMPLETE
##
## ABO - MAL vs LAL
## Number of target genes: 21
## Number of TFs (or genes as TFS): 22258
## names of condition 1: ABO_008__MAL, ABO_066__MAL, ABO_088__MAL, ABO_096__MAL, ABO_186__MAL
## names of condition 2: ABO_052__LAL, ABO_112__LAL, ABO_136__LAL, ABO_184__LAL, ABO_193__LAL
## Number of excluded genes (within condition SD == 0): 3375
## Running RIF...
## Running RIF... COMPLETE
##
##
## ******************* End of - ABO *******************
##
##
## ******************* Start of - DUO *******************
##
## DUO - LR vs MAL
## Number of target genes: 789
## Number of TFs (or genes as TFS): 22258
## names of condition 1: DUO_004__LR, DUO_022__LR, DUO_032__LR, DUO_079__LR, DUO_149__LR
## names of condition 2: DUO_008__MAL, DUO_066__MAL, DUO_088__MAL, DUO_096__MAL, DUO_186__MAL
## Number of excluded genes (within condition SD == 0): 2520
## Running RIF...
## Running RIF... COMPLETE
##
## DUO - LR vs LAL
## Number of target genes: 75
## Number of TFs (or genes as TFS): 22258
## names of condition 1: DUO_004__LR, DUO_022__LR, DUO_032__LR, DUO_079__LR, DUO_149__LR
## names of condition 2: DUO_052__LAL, DUO_112__LAL, DUO_136__LAL, DUO_184__LAL, DUO_193__LAL
## Number of excluded genes (within condition SD == 0): 2577
## Running RIF...
## Running RIF... COMPLETE
##
## DUO - MAL vs LAL
## Number of target genes: 210
## Number of TFs (or genes as TFS): 22258
## names of condition 1: DUO_008__MAL, DUO_066__MAL, DUO_088__MAL, DUO_096__MAL, DUO_186__MAL
## names of condition 2: DUO_052__LAL, DUO_112__LAL, DUO_136__LAL, DUO_184__LAL, DUO_193__LAL
## Number of excluded genes (within condition SD == 0): 2571
## Running RIF...
## Running RIF... COMPLETE
##
##
## ******************* End of - DUO *******************
##
##
## ******************* Start of - RUM *******************
##
## RUM - LR vs MAL
## Number of target genes: 487
## Number of TFs (or genes as TFS): 22258
## names of condition 1: RUM_004__LR, RUM_022__LR, RUM_032__LR, RUM_079__LR, RUM_149__LR
## names of condition 2: RUM_008__MAL, RUM_066__MAL, RUM_088__MAL, RUM_096__MAL, RUM_186__MAL
## Number of excluded genes (within condition SD == 0): 3912
## Running RIF...
## Running RIF... COMPLETE
##
## RUM - LR vs LAL
## Number of target genes: 43
## Number of TFs (or genes as TFS): 22258
## names of condition 1: RUM_004__LR, RUM_022__LR, RUM_032__LR, RUM_079__LR, RUM_149__LR
## names of condition 2: RUM_052__LAL, RUM_112__LAL, RUM_136__LAL, RUM_184__LAL, RUM_193__LAL
## Number of excluded genes (within condition SD == 0): 3799
## Running RIF...
## Running RIF... COMPLETE
##
## RUM - MAL vs LAL
## Number of target genes: 360
## Number of TFs (or genes as TFS): 22258
## names of condition 1: RUM_008__MAL, RUM_066__MAL, RUM_088__MAL, RUM_096__MAL, RUM_186__MAL
## names of condition 2: RUM_052__LAL, RUM_112__LAL, RUM_136__LAL, RUM_184__LAL, RUM_193__LAL
## Number of excluded genes (within condition SD == 0): 3901
## Running RIF...
## Running RIF... COMPLETE
##
##
## ******************* End of - RUM *******************
##
##
## ******************* Start of - LIV *******************
##
## LIV - LR vs MAL
## Number of target genes: 62
## Number of TFs (or genes as TFS): 22258
## names of condition 1: LIV_004__LR, LIV_022__LR, LIV_032__LR, LIV_079__LR, LIV_149__LR
## names of condition 2: LIV_008__MAL, LIV_066__MAL, LIV_088__MAL, LIV_096__MAL, LIV_186__MAL
## Number of excluded genes (within condition SD == 0): 3399
## Running RIF...
## Running RIF... COMPLETE
##
## LIV - LR vs LAL
## Number of target genes: 288
## Number of TFs (or genes as TFS): 22258
## names of condition 1: LIV_004__LR, LIV_022__LR, LIV_032__LR, LIV_079__LR, LIV_149__LR
## names of condition 2: LIV_052__LAL, LIV_112__LAL, LIV_136__LAL, LIV_184__LAL, LIV_193__LAL
## Number of excluded genes (within condition SD == 0): 3585
## Running RIF...
## Running RIF... COMPLETE
##
## LIV - MAL vs LAL
## Number of target genes: 716
## Number of TFs (or genes as TFS): 22258
## names of condition 1: LIV_008__MAL, LIV_066__MAL, LIV_088__MAL, LIV_096__MAL, LIV_186__MAL
## names of condition 2: LIV_052__LAL, LIV_112__LAL, LIV_136__LAL, LIV_184__LAL, LIV_193__LAL
## Number of excluded genes (within condition SD == 0): 3541
## Running RIF...
## Running RIF... COMPLETE
##
##
## ******************* End of - LIV *******************