Return the most/less variant sites of a dataframe or a RiboClass

Usage

get_variant_sites(
  ribo,
  n = NULL,
  type_of_variant = "most",
  only_annotated = TRUE
)

Arguments

ribo: a RiboClass object.
n: Number of top sites to return.
type_of_variant: Either "less" or "most", to select the top n less variant sites or the top n most variant sites respectively.
only_annotated: (RiboClass only) Check variability only among annotated sites. Ignored when df is a dataframe.

Value

A dataframe with the n most/less variant sites

Examples

data("ribo_toy")
data("human_methylated")
ribo_toy <- rename_rna(ribo_toy)
ribo_toy <- annotate_site(ribo_toy,human_methylated)
get_variant_sites(ribo = ribo_toy)
#>                  site        S1        S2         S3        S4        S5
#> 28S_Am1310 28S_Am1310 0.0000000 0.0000000 0.01134216 0.0000000 0.0000000
#> 28S_Gm4607 28S_Gm4607 0.9146472 0.7968187 0.77452668 0.8580486 0.5416635
#> 28S_Gm4593 28S_Gm4593 0.6548805 0.8185865 0.61141927 0.8210696 0.8796136
#> 28S_Um4590 28S_Um4590 0.6743740 0.6292835 0.37707688 0.5174814 0.7131602
#> 28S_Am2774 28S_Am2774 0.9321135 0.8001096 0.76273528 0.6723747 0.6951323
#> 28S_Gm4588 28S_Gm4588 0.9584463 0.8464707 0.94746670 0.8780584 0.6547637
#> 18S_Gm1447 18S_Gm1447 0.9137180 0.8577625 0.90624695 0.7951952 0.6319754
#> 28S_Cm1868 28S_Cm1868 0.9433886 0.8860289 0.70755897 0.8578247 0.7515334
#> 18S_Am576   18S_Am576 0.7737609 0.9224953 0.96262458 0.9224806 0.9093625
#> 18S_Cm1272 18S_Cm1272 0.8648843 0.7675112 0.80444568 0.7947909 0.7094644
#> 28S_Gm4020 28S_Gm4020 0.9498330 0.9408368 0.90054153 0.8882309 0.7126154
#> 28S_Gm2863 28S_Gm2863 0.8946672 0.8861210 0.88665694 0.8644288 0.8365101
#> 28S_Gm3606 28S_Gm3606 0.9403992 0.9051641 0.95128737 0.8803363 0.8757366
#> 28S_Cm2848 28S_Cm2848 0.8663283 0.9312575 0.90639002 0.9236443 0.8930689
#> 28S_Cm4426 28S_Cm4426 0.9880276 0.9624858 0.96296296 0.9447273 0.8032184
#> 28S_Gm1303 28S_Gm1303 0.9125155 0.8199730 0.91398866 0.7808545 0.8208420
#> 18S_Cm174   18S_Cm174 0.9119119 0.8668456 0.88068864 0.8173501 0.7939012
#> 28S_Cm1327 28S_Cm1327 0.9195186 0.8758403 0.87758887 0.8650970 0.8075314
#> 28S_Gm3723 28S_Gm3723 0.8962343 0.8658188 0.91254094 0.8659218 0.7694043
#> 28S_Am3764 28S_Am3764 0.9160839 0.8651212 0.93360046 0.8461538 0.9065975
#>                   S6        S7        S8        S9       S10       S11
#> 28S_Am1310 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
#> 28S_Gm4607 0.6809293 0.6793199 0.8965853 0.8678437 0.9128514 0.8701392
#> 28S_Gm4593 0.7533128 0.8320666 0.6718004 0.6039262 0.6580059 0.6447665
#> 28S_Um4590 0.6357630 0.5902990 0.6466699 0.5832570 0.7077240 0.6050354
#> 28S_Am2774 0.8063538 0.8026389 0.9070491 0.9263572 0.9365647 0.9252246
#> 28S_Gm4588 0.8986765 0.9059829 0.9442231 0.9256655 0.9406554 0.9387978
#> 18S_Gm1447 0.8687242 0.8356861 0.9016198 0.8993957 0.9136080 0.9076239
#> 28S_Cm1868 0.8945420 0.8468489 0.9304794 0.9084319 0.9291232 0.9224108
#> 18S_Am576  0.9448698 0.9155496 0.8330813 0.8865031 0.7987087 0.8150155
#> 18S_Cm1272 0.7804954 0.6661321 0.8571706 0.8362194 0.8190469 0.8250377
#> 28S_Gm4020 0.8726274 0.8813773 0.9417737 0.9205847 0.9149801 0.9307817
#> 28S_Gm2863 0.8950860 0.7250750 0.9047229 0.8664554 0.8373984 0.8151388
#> 28S_Gm3606 0.8962940 0.7536932 0.9263119 0.9295050 0.9229625 0.9187079
#> 28S_Cm2848 0.9378386 0.8911175 0.8985404 0.8799747 0.8089185 0.8133739
#> 28S_Cm4426 0.9783984 0.9636864 0.9792910 0.9791462 0.9726243 0.9742669
#> 28S_Gm1303 0.8642304 0.8528610 0.9178763 0.8780410 0.9125189 0.9046797
#> 18S_Cm174  0.8582238 0.8807750 0.9008655 0.9169832 0.8635969 0.7859844
#> 28S_Cm1327 0.8637317 0.8551941 0.9169329 0.8849945 0.9004181 0.9073924
#> 28S_Gm3723 0.8886241 0.8857796 0.8931605 0.8733850 0.8842931 0.8869016
#> 28S_Am3764 0.9352569 0.8618421 0.8786280 0.9228442 0.9228792 0.8747554
#>                   S12      RNA1      RNA2
#> 28S_Am1310 0.01266131 0.2480990 0.4021636
#> 28S_Gm4607 0.86288210 0.8526672 0.8606764
#> 28S_Gm4593 0.55256116 0.7531421 0.7238179
#> 28S_Um4590 0.56590427 0.7209640 0.7123554
#> 28S_Am2774 0.92049175 0.8051618 0.8255214
#> 28S_Gm4588 0.93250878 0.9207541 0.9284497
#> 18S_Gm1447 0.90245294 0.8688009 0.8825684
#> 28S_Cm1868 0.94075414 0.9253045 0.9175618
#> 18S_Am576  0.81790406 0.9658725 0.9621335
#> 18S_Cm1272 0.83827006 0.8754211 0.8865737
#> 28S_Gm4020 0.92504651 0.9520969 0.9472799
#> 28S_Gm2863 0.86351991 0.9130369 0.9263136
#> 28S_Gm3606 0.91856444 0.9332658 0.9493889
#> 28S_Cm2848 0.82692308 0.9520841 0.9538337
#> 28S_Cm4426 0.96825397 0.9759433 0.9803154
#> 28S_Gm1303 0.90504018 0.9133510 0.9086230
#> 18S_Cm174  0.90818966 0.9104088 0.9045945
#> 28S_Cm1327 0.90408922 0.9453061 0.9222474
#> 28S_Gm3723 0.86924090 0.8868730 0.8806376
#> 28S_Am3764 0.94806694 0.8914334 0.9392550