Print the top-n rows for each ChEA3 collection
Usage
displayTopN(
results,
n = 10,
columns = c("Rank", "TF", "Scaled Rank", "Set_name", "Intersect", "Score",
"FET p-value", "FDR", "Odds Ratio")
)Arguments
- results
A named list of data frames (the output of
queryChEA3()).- n
Number of rows to show per table (default: 10).
- columns
Optional character vector of column names to display (keeps intersection with what's present in each data frame).
Value
(Invisibly) a named list of data frames, each truncated to the first
n rows (and columns if provided).
Examples
# \donttest{
genes <- c("TP53", "MYC", "STAT3", "FOXO1", "BRCA1")
results <- queryChEA3(genes, verbose = FALSE)
# Display top 10 TFs from each collection
displayTopN(results)
#> Top 10 per collection
#> ──────────────────────────────
#> ► Integrated Results
#> ✔ Mean Rank - Average integrated ranks across libraries
#> Rank TF Score
#> 1 ZBTB24 48.33
#> 2 CSRNP1 66.00
#> 3 FOSL2 66.80
#> 4 RUNX1 73.80
#> 5 ETS2 79.75
#> 6 ANHX 86.00
#> 7 MYB 92.50
#> 8 KLF15 110.00
#> 9 POU5F1B 111.50
#> 10 ELF1 113.40
#>
#> ✔ Top Rank - Top integrated rank across libraries
#> Rank TF Score
#> 1 ZBTB24 0.0006143
#> 2 HIVEP1 0.0006223
#> 3 SRY 0.0007123
#> 4 ZXDB 0.0012290
#> 5 MAFF 0.0012450
#> 6 MYOD1 0.0014250
#> 7 ZNF266 0.0018430
#> 8 ZNF800 0.0018670
#> 9 AR 0.0021370
#> 10 ZNF575 0.0024570
#>
#> ────────────────────
#> ► ChIP-Seq
#> ✔ ENCODE - Interactions mined from the ENCODE project
#> Rank TF Scaled Rank Set_name Intersect FET p-value FDR
#> 1 CEBPB 0.008475 CEBPB_C2C12_MM9 3 0.009772 0.59
#> 2 CEBPD 0.016950 CEBPD_K562_HG19 2 0.018070 0.59
#> 3 ZNF384 0.025420 ZNF384_CH12LX_MM9 3 0.019260 0.59
#> 4 IRF3 0.033900 IRF3_HELAS3_HG19 3 0.019570 0.59
#> 5 E2F4 0.042370 E2F4_CH12LX_MM9 3 0.021010 0.59
#> 6 ATF2 0.050850 ATF2_H1HESC_HG19 3 0.021370 0.59
#> 7 CTCF 0.059320 CTCF_OSTEOBLAST_HG19 3 0.022910 0.59
#> 8 ATF3 0.067800 ATF3_A549_HG19 3 0.023260 0.59
#> 9 JUND 0.076270 JUND_GM12878_HG19 2 0.023640 0.59
#> 10 MXI1 0.084750 MXI1_H1HESC_HG19 3 0.023800 0.59
#> Odds Ratio
#> 9.358
#> 12.580
#> 7.167
#> 7.120
#> 6.919
#> 6.871
#> 6.680
#> 6.639
#> 10.850
#> 6.577
#>
#> ✔ ReMap - Interactions mined from the ReMap project
#> Rank TF Scaled Rank Set_name Intersect FET p-value FDR Odds Ratio
#> 1 EOMES 0.003367 EOMES 3 0.01318 0.651 8.331
#> 2 FOXP1 0.006734 FOXP1 3 0.01337 0.651 8.285
#> 3 POU5F1 0.010100 POU5F1 3 0.01344 0.651 8.268
#> 4 KMT2B 0.013470 KMT2B 2 0.07561 0.651 5.558
#> 5 RFX2 0.016840 RFX2 2 0.07569 0.651 5.554
#> 6 DEAF1 0.020200 DEAF1 2 0.07595 0.651 5.543
#> 7 KLF3 0.023570 KLF3 2 0.07595 0.651 5.543
#> 8 TBXT 0.026940 TBXT 2 0.07604 0.651 5.539
#> 9 CXXC4 0.030300 CXXC4 2 0.07604 0.651 5.539
#> 10 BACH2 0.033670 BACH2 2 0.07604 0.651 5.539
#>
#> ✔ Literature - Interactions mined from the literature
#> Rank TF Scaled Rank Set_name Intersect
#> 1 EGR1 0.006098 EGR1_19374776_CHIPCHIP_THP1_HUMAN 2
#> 2 ESR1 0.012200 ESR1_15608294_CHIPCHIP_MCF7_HUMAN 2
#> 3 NANOG 0.018290 NANOG_18347094_CHIPCHIP_MESC_MOUSE 4
#> 4 E2F4 0.024390 E2F4_17652178_CHIPCHIP_JURKAT_HUMAN 3
#> 5 STAT4 0.030490 STAT4_19710469_CHIPCHIP_TH1_MOUSE 3
#> 6 BACH1 0.036590 BACH1_22875853_CHIPPCR_HELAANDSCP4_HUMAN 3
#> 7 STAT3 0.042680 STAT3_22323479_CHIPSEQ_MACROPHAGE_MOUSE 1
#> 8 PPARD 0.048780 PPARD_23208498_CHIPSEQ_MDAMB231_HUMAN 2
#> 9 E2F7 0.054880 E2F7_22180533_CHIPSEQ_HELA_HUMAN 1
#> 10 POU5F1 0.060980 POU5F1_16153702_CHIPCHIP_HESC_HUMAN 2
#> FET p-value FDR Odds Ratio
#> 0.0002281 0.0589 123.000
#> 0.0003840 0.0589 94.090
#> 0.0026980 0.2410 10.120
#> 0.0031380 0.2410 14.330
#> 0.0088110 0.3490 9.738
#> 0.0100300 0.3490 9.264
#> 0.0101400 0.3490 121.200
#> 0.0106100 0.3490 16.770
#> 0.0134000 0.3490 90.890
#> 0.0141500 0.3490 14.360
#>
#> ────────────────────
#> ► Coexpression
#> ✔ ARCHS4 - TF-target coexpression in the ARCHS4 dataset
#> Rank TF Scaled Rank Set_name Intersect FET p-value FDR
#> 1 ZBTB24 0.0006143 ZBTB24_ARCHS4_PEARSON 1 0.08493 1
#> 2 ZXDB 0.0012290 ZXDB_ARCHS4_PEARSON 1 0.08493 1
#> 3 ZNF266 0.0018430 ZNF266_ARCHS4_PEARSON 1 0.08493 1
#> 4 ZNF575 0.0024570 ZNF575_ARCHS4_PEARSON 1 0.08493 1
#> 5 FOXP3 0.0030710 FOXP3_ARCHS4_PEARSON 1 0.08520 1
#> 6 FOXO1 0.0036860 FOXO1_ARCHS4_PEARSON 1 0.08520 1
#> 7 ZNF395 0.0043000 ZNF395_ARCHS4_PEARSON 1 0.08520 1
#> 8 PRDM9 0.0049140 PRDM9_ARCHS4_PEARSON 1 0.08520 1
#> 9 ZSCAN4 0.0055280 ZSCAN4_ARCHS4_PEARSON 1 0.08520 1
#> 10 ATF7 0.0061430 ATF7_ARCHS4_PEARSON 1 0.08520 1
#> Odds Ratio
#> 13.46
#> 13.46
#> 13.46
#> 13.46
#> 13.42
#> 13.42
#> 13.42
#> 13.42
#> 13.42
#> 13.42
#>
#> ✔ GTEx - TF-target coexpression in the GTEx dataset
#> Rank TF Scaled Rank Set_name Intersect FET p-value FDR Odds Ratio
#> 1 HIVEP1 0.0006223 HIVEP1 3 0.0001694 0.272 40.39
#> 2 MAFF 0.0012450 MAFF 2 0.0042970 0.999 27.02
#> 3 ZNF800 0.0018670 ZNF800 2 0.0043250 0.999 26.93
#> 4 FOSL2 0.0024890 FOSL2 2 0.0043520 0.999 26.84
#> 5 ETV6 0.0031110 ETV6 2 0.0043520 0.999 26.84
#> 6 TGIF1 0.0037340 TGIF1 2 0.0043520 0.999 26.84
#> 7 ETS2 0.0043560 ETS2 2 0.0043520 0.999 26.84
#> 8 KLF15 0.0049780 KLF15 1 0.0843900 1.000 13.56
#> 9 EGR1 0.0056000 EGR1 1 0.0846600 1.000 13.51
#> 10 FOXD4L5 0.0062230 FOXD4L5 1 0.0846600 1.000 13.51
#>
#> ────────────────────
#> ► Co-occurrence
#> ✔ Enrichr - TF-target co-occurrence in Enrichr queries
#> Rank TF Scaled Rank Set_name Intersect FET p-value FDR Odds Ratio
#> 1 SRY 0.0007123 SRY 5 1.465e-07 7.98e-06 69.19
#> 2 MYOD1 0.0014250 MYOD1 5 1.489e-07 7.98e-06 68.95
#> 3 AR 0.0021370 AR 5 1.489e-07 7.98e-06 68.95
#> 4 NR5A1 0.0028490 NR5A1 5 1.489e-07 7.98e-06 68.95
#> 5 PGR 0.0035610 PGR 5 1.514e-07 7.98e-06 68.71
#> 6 TP73 0.0042740 TP73 5 1.514e-07 7.98e-06 68.71
#> 7 E2F3 0.0049860 E2F3 5 1.514e-07 7.98e-06 68.71
#> 8 SMAD3 0.0056980 SMAD3 5 1.514e-07 7.98e-06 68.71
#> 9 ESR1 0.0064100 ESR1 5 1.514e-07 7.98e-06 68.71
#> 10 ARNT 0.0071230 ARNT 5 1.514e-07 7.98e-06 68.71
#>
#> ────────────────────
# Display only top 5 with specific columns
displayTopN(results, n = 5, columns = c("Rank", "TF", "Score", "FDR"))
#> Top 5 per collection
#> ──────────────────────────────
#> ► Integrated Results
#> ✔ Mean Rank - Average integrated ranks across libraries
#> Rank TF Score
#> 1 ZBTB24 48.33
#> 2 CSRNP1 66.00
#> 3 FOSL2 66.80
#> 4 RUNX1 73.80
#> 5 ETS2 79.75
#>
#> ✔ Top Rank - Top integrated rank across libraries
#> Rank TF Score
#> 1 ZBTB24 0.0006143
#> 2 HIVEP1 0.0006223
#> 3 SRY 0.0007123
#> 4 ZXDB 0.0012290
#> 5 MAFF 0.0012450
#>
#> ────────────────────
#> ► ChIP-Seq
#> ✔ ENCODE - Interactions mined from the ENCODE project
#> Rank TF FDR
#> 1 CEBPB 0.59
#> 2 CEBPD 0.59
#> 3 ZNF384 0.59
#> 4 IRF3 0.59
#> 5 E2F4 0.59
#>
#> ✔ ReMap - Interactions mined from the ReMap project
#> Rank TF FDR
#> 1 EOMES 0.651
#> 2 FOXP1 0.651
#> 3 POU5F1 0.651
#> 4 KMT2B 0.651
#> 5 RFX2 0.651
#>
#> ✔ Literature - Interactions mined from the literature
#> Rank TF FDR
#> 1 EGR1 0.0589
#> 2 ESR1 0.0589
#> 3 NANOG 0.2410
#> 4 E2F4 0.2410
#> 5 STAT4 0.3490
#>
#> ────────────────────
#> ► Coexpression
#> ✔ ARCHS4 - TF-target coexpression in the ARCHS4 dataset
#> Rank TF FDR
#> 1 ZBTB24 1
#> 2 ZXDB 1
#> 3 ZNF266 1
#> 4 ZNF575 1
#> 5 FOXP3 1
#>
#> ✔ GTEx - TF-target coexpression in the GTEx dataset
#> Rank TF FDR
#> 1 HIVEP1 0.272
#> 2 MAFF 0.999
#> 3 ZNF800 0.999
#> 4 FOSL2 0.999
#> 5 ETV6 0.999
#>
#> ────────────────────
#> ► Co-occurrence
#> ✔ Enrichr - TF-target co-occurrence in Enrichr queries
#> Rank TF FDR
#> 1 SRY 7.98e-06
#> 2 MYOD1 7.98e-06
#> 3 AR 7.98e-06
#> 4 NR5A1 7.98e-06
#> 5 PGR 7.98e-06
#>
#> ────────────────────
# }