A list containing data used by RLSeq functions. It can also be useful
for checking the available modes and genomes in RLSeq. See also the
data-raw/auxdata.R script that was used to create it.
auxdataAn object of class list of length 12.
A named list containing the following entries:
db_cols
A tbl with colors associated with each database in RLHub
useful for plotting. See also RLHub::annotations.
annotypes
A tbl containing the annotation databases and annotation types
available from RLBase. See also RLHub::annotations.
ip_cols
A tbl containing the colors associated with each "Immunoprecipitation
type" (ip_type) in RLBase. See also RLHub::rlbase_samples.
mode_cols
A tbl containing the colors associated with each R-loop mapping
mode in RLHub::rlbase_samples.
heat_cols
A tbl containing the colors associated with user-supplied data and
RLBase data when running corrHeatmap.
label_cols
A tbl containing the colors associated with the labels in
RLBase.
See also RLHub::rlbase_samples.
prediction_cols
A tbl containing the colors associated with the predictions in
RLBase.
See also RLHub::rlbase_samples.
prediction_label_cols
A tbl containing the colors associated with the prediction-label
combinations in
RLBase.
See also RLHub::rlbase_samples.
available_modes
A tbl containing the modes available in RLBase and associated metadata.
See also RLHub::rlbase_samples.
available_genomes
A character showing all the official UCSC genomes available for use
with RLSeq. See also available_genomes.
misc_modes
A character showing the R-loop mapping modes that are lumped into
the 'misc' category for simplification of plotting.
auxdata
#> $db_cols
#> # A tibble: 20 × 2
#> db col
#> <chr> <chr>
#> 1 Centromeres #876800
#> 2 CNA #9546C0
#> 3 Cohesin #BA3D5D
#> 4 CpG_Islands #00878E
#> 5 Encode_CREs #AD34B0
#> 6 Encode_Histone #BD317E
#> 7 encodeTFBS #B44741
#> 8 G4Qexp #9A5E00
#> 9 G4Qpred #007AB8
#> 10 knownGene_RNAs #006CC4
#> 11 Microsatellite #6F7100
#> 12 PolyA #0082A6
#> 13 RBP_ChIP #A95300
#> 14 RBP_eCLiP #6A5AC7
#> 15 Repeat_Masker #007E00
#> 16 skewr #4D7800
#> 17 snoRNA_miRNA_scaRNA #008650
#> 18 Splice_Events #BA2C9A
#> 19 Transcript_Features #00831F
#> 20 tRNAs #008872
#>
#> $annotypes
#> # A tibble: 638 × 2
#> db type
#> <chr> <chr>
#> 1 Centromeres Centromeres
#> 2 CNA 0
#> 3 CNA 1
#> 4 CNA 2
#> 5 CNA 3
#> 6 CNA 4
#> 7 Cohesin STAG1
#> 8 Cohesin STAG2
#> 9 CpG_Islands CpG_Islands
#> 10 Encode_CREs CTCF
#> # … with 628 more rows
#> # ℹ Use `print(n = ...)` to see more rows
#>
#> $rlbps
#> # A tibble: 788 × 5
#> geneName NADEL.2015 WANG.2018 CRISTINI.2018 combinedScore
#> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 DDX21 0.9 0 0.968 1.87
#> 2 DHX9 0.85 0.0635 0.831 1.74
#> 3 HNRNPR 1 0 0.731 1.73
#> 4 ILF3 0.85 0.0708 0.749 1.67
#> 5 NKRF 0 1 0.636 1.64
#> 6 PDCD11 0 1 0.633 1.63
#> 7 PWP1 0 1 0.620 1.62
#> 8 SRPK1 0 1 0.457 1.46
#> 9 PWP2 0 0.960 0.472 1.43
#> 10 NPM3 0 1 0.397 1.40
#> # … with 778 more rows
#> # ℹ Use `print(n = ...)` to see more rows
#>
#> $ip_cols
#> # A tibble: 3 × 3
#> ip_type POS NEG
#> <chr> <chr> <chr>
#> 1 S9.6 #2E294E #2E2C3B
#> 2 dRNH #C1292E #955253
#> 3 Other #F3B700 #D8BC94
#>
#> $mode_cols
#> # A tibble: 11 × 2
#> mode col
#> <chr> <chr>
#> 1 MapR #FE7267
#> 2 qDRIP #DC8E00
#> 3 ssDRIP #A3A600
#> 4 RDIP #24B700
#> 5 sDRIP #00C27A
#> 6 DRIPc #00C2C8
#> 7 DRIP #00B2FF
#> 8 RLCnT-S96 #938DFF
#> 9 RLCnT-HBD #EF62FB
#> 10 R-ChIP #FF58BF
#> 11 misc #8f8f8f
#>
#> $heat_cols
#> # A tibble: 2 × 2
#> selected col
#> <chr> <chr>
#> 1 RLBase #e0dede
#> 2 user_selected #2c408a
#>
#> $label_cols
#> # A tibble: 2 × 2
#> label col
#> <chr> <chr>
#> 1 POS #e0dede
#> 2 NEG #8a2c2c
#>
#> $prediction_cols
#> # A tibble: 2 × 2
#> prediction col
#> <chr> <chr>
#> 1 POS #e0dede
#> 2 NEG #8a2c2c
#>
#> $prediction_label_cols
#> NEG_NEG NEG_POS POS_NEG POS_POS
#> "#8a2c2c" "#A76767" "#7aa4c4" "#2270ab"
#>
#> $available_modes
#> # A tibble: 20 × 6
#> mode family ip_type strand_specific moeity bisulfite_seq
#> <chr> <chr> <chr> <lgl> <chr> <lgl>
#> 1 DRIPc DRIP S9.6 TRUE RNA FALSE
#> 2 DRIP DRIP S9.6 FALSE DNA FALSE
#> 3 sDRIP DRIP S9.6 TRUE DNA FALSE
#> 4 ssDRIP DRIP S9.6 TRUE DNA FALSE
#> 5 DRNA Other None FALSE RNA FALSE
#> 6 MapR MapR dRNH FALSE DNA FALSE
#> 7 m6A-DIP RDIP RNA-m6A FALSE DNA FALSE
#> 8 DRIVE Other dRNH FALSE RNA FALSE
#> 9 RLCnT-HBD RLCnT dRNH TRUE DNA FALSE
#> 10 RLCnT-S96 RLCnT S9.6 TRUE DNA FALSE
#> 11 DRIPc-HBD DRIP dRNH TRUE RNA FALSE
#> 12 qDRIP DRIP S9.6 TRUE DNA FALSE
#> 13 RDIP RDIP S9.6 TRUE RNA FALSE
#> 14 DRIP-RNA-Seq DRIP S9.6 TRUE RNA FALSE
#> 15 DREAM Other None TRUE RNA FALSE
#> 16 R-ChIP R-ChIP dRNH TRUE DNA FALSE
#> 17 RR-ChIP R-ChIP dRNH TRUE RNA FALSE
#> 18 RNH-CnR MapR dRNH FALSE DNA FALSE
#> 19 S1-DRIP DRIP S9.6 FALSE DNA FALSE
#> 20 BisMapR MapR dRNH TRUE DNA FALSE
#>
#> $available_genomes
#> [1] "canFam3" "ce10" "ce11" "ce6" "ci3" "danRer10"
#> [7] "danRer11" "danRer7" "dm6" "fr3" "galGal4" "galGal5"
#> [13] "galGal6" "gorGor3" "gorGor4" "gorGor5" "hg19" "hg38"
#> [19] "mm10" "mm9" "panPan1" "panTro3" "panTro4" "panTro5"
#> [25] "panTro6" "papAnu2" "rheMac3" "rheMac8" "rn5" "rn6"
#> [31] "sacCer2" "sacCer3" "susScr11" "susScr3" "taeGut2" "tetNig2"
#> [37] "xenTro3" "xenTro7" "xenTro9"
#>
#> $misc_modes
#> [1] "BisMapR" "DREAM" "DRIP-RNA-Seq" "DRIPc-HBD" "DRIVE"
#> [6] "DRNA" "m6A-DIP" "RNH-CnR" "RR-ChIP" "S1-DRIP"
#>