Relative difference of DESeq results

resultsDiff(x, y, ...)

# S4 method for DESeqResults,DESeqResults
resultsDiff(
  x,
  y,
  col = c("log2FoldChange", "stat"),
  deg = c("no", "intersect", "union"),
  alpha = NULL,
  lfcThreshold = NULL,
  direction = c("both", "up", "down")
)

# S4 method for DESeqAnalysis,missingOrNULL
resultsDiff(x, y = NULL, i, j, lfcShrink = TRUE, ...)

Arguments

x

Object.

y

Object.

...

Additional arguments.

col

character(1). Column to use for difference calculation (subtraction). Note that x/i represents A and y/j B in A - B calculation.

deg

character(1).

  • "no": Return all genes, corresponding to original row names order.

  • "intersect": Return only genes called as DE in both contrasts.

  • "union": Return genes called as DE in either contrast.

alpha

numeric(1) or NULL. Adjusted P value ("alpha") cutoff. If left NULL, will use the cutoff defined in the object.

lfcThreshold

numeric(1) or NULL. Log fold change ratio (base 2) cutoff threshold. If left NULL, will use the cutoff defined in the object.

direction

character(1). Include "both", "up", or "down" directions.

i

Indices specifying elements to extract or replace. Indices are numeric or character vectors, empty (missing), or NULL.

For more information:

help(topic = "Extract", package = "base")
j

Indices specifying elements to extract or replace. Indices are numeric or character vectors, empty (missing), or NULL.

For more information:

help(topic = "Extract", package = "base")
lfcShrink

logical(1). Use shrunken log2 fold change (LFC) values.

Value

Named numeric. Names correspond to the genes (row names).

Functions

  • resultsDiff,DESeqAnalysis,missingOrNULL-method: Passes arguments to DESeqResults method.

Note

Updated 2019-12-17.

Examples

data(deseq) ## DESeqResults ==== x <- results(deseq, i = 1L)
#> condition_B_vs_A (unshrunken LFC)
y <- results(deseq, i = 2L)
#> treatment_D_vs_C (unshrunken LFC)
resultsDiff(x = x, y = y)
#> Calculating relative difference of 'log2FoldChange'.
#> gene001 gene002 gene003 gene004 gene005 gene006 #> 0.135429419 0.998536314 0.763499604 -2.142890353 0.114218708 -1.607047388 #> gene007 gene008 gene009 gene010 gene011 gene012 #> -2.939731586 -0.526484303 0.236730899 -1.511212910 -0.829753533 3.060766630 #> gene013 gene014 gene015 gene016 gene017 gene018 #> -0.620917722 1.484750928 0.278251727 0.581340878 -2.403994904 -0.004540839 #> gene019 gene020 gene021 gene022 gene023 gene024 #> -0.122104982 0.394530719 0.629255693 0.278199106 -0.726850132 -1.008569200 #> gene025 gene026 gene027 gene028 gene029 gene030 #> 0.338402342 0.943227343 1.856925865 2.947011701 -0.552418060 2.973923079 #> gene031 gene032 gene033 gene034 gene035 gene036 #> -0.275888530 -3.263337504 0.261257433 -0.706321703 -2.144035072 -0.410440054 #> gene037 gene038 gene039 gene040 gene041 gene042 #> 0.143855066 -1.057093971 -1.325673480 0.972879217 -3.906341676 -0.084882877 #> gene043 gene044 gene045 gene046 gene047 gene048 #> 1.332057955 -1.159007363 0.211213044 0.394284926 -0.537981055 0.838287229 #> gene049 gene050 gene051 gene052 gene053 gene054 #> -3.097811366 -0.461236625 0.537142067 -0.059455809 -1.970548399 0.862244123 #> gene055 gene056 gene057 gene058 gene059 gene060 #> 1.669786803 3.378546101 2.376824552 1.103561300 -2.538256728 -1.376892644 #> gene061 gene062 gene063 gene064 gene065 gene066 #> 0.628332216 1.247987382 0.712635069 -2.410204919 0.412006035 -0.521643910 #> gene067 gene068 gene069 gene070 gene071 gene072 #> 2.010138991 0.520042935 -0.490243593 -0.978651703 0.822776872 -3.275548878 #> gene073 gene074 gene075 gene076 gene077 gene078 #> -0.152667019 -0.099903125 -0.376039386 -0.239093121 3.357648398 1.286998050 #> gene079 gene080 gene081 gene082 gene083 gene084 #> 0.110655772 1.851781384 -0.249063656 1.146170342 -1.042732860 -1.608784383 #> gene085 gene086 gene087 gene088 gene089 gene090 #> -3.451070577 -1.668388592 0.787902233 1.528894233 -0.177587628 -0.280531304 #> gene091 gene092 gene093 gene094 gene095 gene096 #> 1.724766602 -1.504265309 -4.069293353 0.096039843 -1.059212295 0.984766740 #> gene097 gene098 gene099 gene100 gene101 gene102 #> -4.128092515 -1.842973337 -0.920986185 2.409066062 1.364686949 2.883312037 #> gene103 gene104 gene105 gene106 gene107 gene108 #> 0.674964202 -0.919981767 -1.346785124 -0.027219461 -0.568062440 -0.494808270 #> gene109 gene110 gene111 gene112 gene113 gene114 #> 4.100911664 0.592096455 1.664522228 1.039456901 0.793808319 0.560993081 #> gene115 gene116 gene117 gene118 gene119 gene120 #> -0.004032814 0.238144340 -0.797069506 -0.584891333 -1.579094750 0.031927050 #> gene121 gene122 gene123 gene124 gene125 gene126 #> -1.398488741 0.156008705 2.092805064 -1.228595623 -0.979421379 0.398811070 #> gene127 gene128 gene129 gene130 gene131 gene132 #> 0.014327305 3.760040221 -1.057097757 -1.217057508 1.415188127 -1.965801428 #> gene133 gene134 gene135 gene136 gene137 gene138 #> 0.259181409 0.530204426 -0.953520825 0.902350341 2.811984338 -0.953522181 #> gene139 gene140 gene141 gene142 gene143 gene144 #> -0.144552703 1.242026304 -0.921643136 -1.600436066 -1.202661830 -1.044781587 #> gene145 gene146 gene147 gene148 gene149 gene150 #> -0.113792480 -4.780121444 1.040293678 -0.523895169 -2.293260794 -0.457699815 #> gene151 gene152 gene153 gene154 gene155 gene156 #> -2.987750203 -0.806033661 -1.178259197 -0.198374743 3.298193043 0.601999037 #> gene157 gene158 gene159 gene160 gene161 gene162 #> -0.015917679 0.962188346 -1.021948326 -0.458889727 -0.178925779 -0.781423269 #> gene163 gene164 gene165 gene166 gene167 gene168 #> 0.075404699 3.220767686 0.704645024 -0.522536227 -0.792762595 2.328173407 #> gene169 gene170 gene171 gene172 gene173 gene174 #> -2.001922026 1.081571693 3.098664494 0.528054592 -1.985855041 -0.890353838 #> gene175 gene176 gene177 gene178 gene179 gene180 #> -0.354540774 4.991187915 0.674958150 -0.202091998 -1.621687814 0.246718501 #> gene181 gene182 gene183 gene184 gene185 gene186 #> 1.431569888 -3.249815185 -3.765930748 -0.694408576 1.642350035 -1.980880137 #> gene187 gene188 gene189 gene190 gene191 gene192 #> -0.569844614 1.517301040 -1.888689567 -2.279152669 -2.004929244 -0.431028927 #> gene193 gene194 gene195 gene196 gene197 gene198 #> -0.857740668 0.143771396 1.229683175 -1.116310429 -0.345826097 3.591278692 #> gene199 gene200 gene201 gene202 gene203 gene204 #> 0.010650502 -0.617596562 0.030364431 1.227494917 0.314499903 -0.366656328 #> gene205 gene206 gene207 gene208 gene209 gene210 #> -3.083329417 -1.115223146 0.388005936 -1.604263613 -1.297867763 1.207298059 #> gene211 gene212 gene213 gene214 gene215 gene216 #> 0.898807167 1.436885149 0.106223245 1.903022342 -0.555835160 0.548824900 #> gene217 gene218 gene219 gene220 gene221 gene222 #> 0.501493465 0.866480733 1.584496217 0.944763892 0.737409049 -0.028156341 #> gene223 gene224 gene225 gene226 gene227 gene228 #> -0.142813265 1.292537344 -0.884760564 4.045755545 0.186224303 1.550543573 #> gene229 gene230 gene231 gene232 gene233 gene234 #> 2.770005711 -0.047067558 0.817072510 -4.848441991 -0.840915547 -1.736438691 #> gene235 gene236 gene237 gene238 gene239 gene240 #> 0.226124194 0.271982576 2.008485734 -0.440415800 -2.502772603 1.567720894 #> gene241 gene242 gene243 gene244 gene245 gene246 #> 0.587401246 -0.836117765 1.665524853 -0.464377512 -0.855067413 -1.205451206 #> gene247 gene248 gene249 gene250 gene251 gene252 #> 0.979355277 1.184603187 -0.731932251 0.210204474 -2.257300861 -0.446552880 #> gene253 gene254 gene255 gene256 gene257 gene258 #> 2.675166385 -1.316889905 -0.604642025 -0.095306619 2.263890766 0.119198847 #> gene259 gene260 gene261 gene262 gene263 gene264 #> -1.705228495 0.609512589 -1.570856214 0.138099614 -0.166628801 0.626028040 #> gene265 gene266 gene267 gene268 gene269 gene270 #> -2.969818366 -1.487221658 1.504565170 -0.655670802 -3.265865332 -0.894104377 #> gene271 gene272 gene273 gene274 gene275 gene276 #> -0.526393560 1.261121138 -2.784793396 -0.043330962 -1.088683222 -0.623163316 #> gene277 gene278 gene279 gene280 gene281 gene282 #> NA 0.478429613 -3.226350551 1.202999505 -0.034630843 -0.098330212 #> gene283 gene284 gene285 gene286 gene287 gene288 #> -0.388587454 0.620374782 -0.170861492 0.910965469 1.880818304 -2.749884974 #> gene289 gene290 gene291 gene292 gene293 gene294 #> -2.074919716 -1.003053162 -2.522421841 0.519834572 1.983727598 -1.219505125 #> gene295 gene296 gene297 gene298 gene299 gene300 #> 1.291034758 0.771948976 1.420236309 -1.563169219 1.390523154 -3.157001188 #> gene301 gene302 gene303 gene304 gene305 gene306 #> 0.995145511 1.305428321 -0.827937905 4.522984645 -1.417095280 -0.170480146 #> gene307 gene308 gene309 gene310 gene311 gene312 #> 0.876907676 0.312887043 0.326072440 -0.238011035 -0.420151474 2.639492484 #> gene313 gene314 gene315 gene316 gene317 gene318 #> -0.996881289 0.006146566 3.303070700 0.277640304 -0.310187288 -2.794823455 #> gene319 gene320 gene321 gene322 gene323 gene324 #> 1.357224380 0.588952875 0.097667669 -0.952159886 -0.891914624 -0.472831408 #> gene325 gene326 gene327 gene328 gene329 gene330 #> 0.916905690 -0.362600241 -0.148887528 -0.526622534 1.774455699 -4.537760463 #> gene331 gene332 gene333 gene334 gene335 gene336 #> 0.809854785 -0.391051450 -0.317781523 -0.614193799 -4.384546250 -0.076599537 #> gene337 gene338 gene339 gene340 gene341 gene342 #> -0.623251901 3.564425696 1.459480747 -0.096705076 0.614996864 -0.607726216 #> gene343 gene344 gene345 gene346 gene347 gene348 #> -1.057097047 -1.393720373 -0.792557601 -0.095306619 -0.123033554 -2.597634332 #> gene349 gene350 gene351 gene352 gene353 gene354 #> 4.675332893 0.864963733 -1.460653353 1.485343605 -0.677576429 -3.735835706 #> gene355 gene356 gene357 gene358 gene359 gene360 #> 1.155851029 -1.442962943 1.328764869 2.221477047 -0.576126564 0.569603856 #> gene361 gene362 gene363 gene364 gene365 gene366 #> -0.637583474 2.380233966 -0.308049076 -1.100317798 -0.010705403 3.027368447 #> gene367 gene368 gene369 gene370 gene371 gene372 #> -1.057100508 -1.033432802 -1.393395063 -1.875522172 -0.245832497 -0.065059408 #> gene373 gene374 gene375 gene376 gene377 gene378 #> -0.149670043 0.942919369 0.309478350 0.353994271 0.393096461 2.113051993 #> gene379 gene380 gene381 gene382 gene383 gene384 #> -5.517859792 -2.438888579 -1.708216048 0.512116310 -0.184676662 0.321003030 #> gene385 gene386 gene387 gene388 gene389 gene390 #> -3.366056073 -1.371153751 0.269776837 1.314349619 0.629009731 -0.744227464 #> gene391 gene392 gene393 gene394 gene395 gene396 #> -0.041820440 -0.704528901 0.165510430 0.107109740 1.135626959 0.216157390 #> gene397 gene398 gene399 gene400 gene401 gene402 #> 3.307611426 -1.677624172 -0.119979547 -0.367770010 -1.568911793 -1.494433513 #> gene403 gene404 gene405 gene406 gene407 gene408 #> 0.514651997 1.787764053 0.028258757 -0.332227165 -1.576205959 0.432481683 #> gene409 gene410 gene411 gene412 gene413 gene414 #> -1.279059242 -1.625261786 -0.066556247 -1.820460723 -1.346737470 -0.544498097 #> gene415 gene416 gene417 gene418 gene419 gene420 #> 0.936715725 0.688346825 2.340425055 -0.104052275 -0.211711174 -0.838048001 #> gene421 gene422 gene423 gene424 gene425 gene426 #> -0.357397463 -3.023981215 0.010728595 -1.457138394 0.589306836 1.103526285 #> gene427 gene428 gene429 gene430 gene431 gene432 #> -0.947106668 0.836328864 -2.859237016 -2.505870975 1.910930989 1.466076010 #> gene433 gene434 gene435 gene436 gene437 gene438 #> 0.322925457 1.846357556 3.950437231 -1.446885666 -1.351216507 0.140444997 #> gene439 gene440 gene441 gene442 gene443 gene444 #> 0.056040900 -1.068742253 -0.259902683 -0.087805680 2.747616228 -4.560490385 #> gene445 gene446 gene447 gene448 gene449 gene450 #> -0.402390143 1.177928013 0.823470662 -1.289542732 1.063256047 -3.194912926 #> gene451 gene452 gene453 gene454 gene455 gene456 #> -1.537105468 1.067733918 0.468905351 0.900843079 0.325531441 -0.431249122 #> gene457 gene458 gene459 gene460 gene461 gene462 #> 0.354439877 -1.321277276 -1.878318315 -1.583642414 -0.933811088 -3.464047706 #> gene463 gene464 gene465 gene466 gene467 gene468 #> -2.936562753 -0.351943280 2.161921690 -0.748147109 -2.977375470 0.811450763 #> gene469 gene470 gene471 gene472 gene473 gene474 #> -0.664559628 -1.502638531 2.155447182 0.368451732 0.204515957 0.113877428 #> gene475 gene476 gene477 gene478 gene479 gene480 #> 0.211396757 -0.674516809 0.991905814 1.872739085 -2.403229560 -0.286098021 #> gene481 gene482 gene483 gene484 gene485 gene486 #> 0.878571995 0.377998787 1.870907757 -1.122368311 -0.820057809 -0.354125039 #> gene487 gene488 gene489 gene490 gene491 gene492 #> 0.866480733 -0.855963467 -2.576960718 1.187377022 -0.843930915 -0.293518064 #> gene493 gene494 gene495 gene496 gene497 gene498 #> 0.972592014 -2.842828849 0.808596202 1.607361638 1.226284171 3.069360165 #> gene499 gene500 #> 0.840007165 -0.737040293
## DESeqAnalysis ==== object <- deseq resultsDiff(object, i = 1L, j = 2L)
#> condition_B_vs_A (shrunken LFC)
#> treatment_D_vs_C (shrunken LFC)
#> Calculating relative difference of 'log2FoldChange'.
#> gene001 gene002 gene003 gene004 gene005 #> 0.6676517264 0.2241710266 0.1687927632 0.0153596933 -0.2239665320 #> gene006 gene007 gene008 gene009 gene010 #> -0.5732946778 -1.8727938184 -0.0183509294 -0.3947941265 -0.0006928087 #> gene011 gene012 gene013 gene014 gene015 #> -0.2704492038 0.1007829424 -0.0785694340 0.1860848260 0.6096471809 #> gene016 gene017 gene018 gene019 gene020 #> -0.0723576694 -0.1542258686 0.0289448553 0.3298941113 0.2147923247 #> gene021 gene022 gene023 gene024 gene025 #> 0.0655920219 0.6473071153 -0.4879692927 -1.2057037011 0.0500677391 #> gene026 gene027 gene028 gene029 gene030 #> 0.1155508969 1.2195259047 2.6089898067 -0.1318270944 1.9619761723 #> gene031 gene032 gene033 gene034 gene035 #> -0.2917950690 -0.3639006028 -0.0522546581 0.1377694993 -1.2908766590 #> gene036 gene037 gene038 gene039 gene040 #> -0.2394997039 -0.0051738129 -0.0701495516 -0.5763582871 0.5564052328 #> gene041 gene042 gene043 gene044 gene045 #> -0.7548740614 0.0140539691 0.5589827000 -0.4771782247 0.0084874762 #> gene046 gene047 gene048 gene049 gene050 #> -0.1766554434 -0.2272478969 0.3204349847 -0.4120338172 -0.4373501837 #> gene051 gene052 gene053 gene054 gene055 #> 0.2961622369 -0.3350745216 -0.2650486563 0.9193906647 1.2002157270 #> gene056 gene057 gene058 gene059 gene060 #> 0.1663868827 1.4803895440 0.3723097991 -0.0153437867 -1.6879788172 #> gene061 gene062 gene063 gene064 gene065 #> 0.4680718592 1.1560177509 0.2843868006 -0.0923404985 0.5618400353 #> gene066 gene067 gene068 gene069 gene070 #> -0.1825125762 0.9849830243 -0.3526421378 0.0860684030 0.5684313837 #> gene071 gene072 gene073 gene074 gene075 #> 0.4043362551 -0.2761173746 -0.0349943452 0.2550471953 -0.2732950143 #> gene076 gene077 gene078 gene079 gene080 #> -0.0210261058 0.0011539291 0.1201983253 -0.0901549177 0.9133997333 #> gene081 gene082 gene083 gene084 gene085 #> 0.4395450270 0.3768848588 -0.1347200295 -1.6144538636 -0.0238326639 #> gene086 gene087 gene088 gene089 gene090 #> -0.5182733670 0.9778342943 0.5174353615 -0.1154349417 -0.4014136037 #> gene091 gene092 gene093 gene094 gene095 #> 0.4661320424 -0.3522304649 -0.2823241790 -0.0934052060 -1.4675002364 #> gene096 gene097 gene098 gene099 gene100 #> 0.3587150400 -0.0179859881 -0.5610244018 -0.7801832628 0.0254020765 #> gene101 gene102 gene103 gene104 gene105 #> 1.1442073430 -0.0471669966 0.2502289897 -0.2395888907 -0.9610439494 #> gene106 gene107 gene108 gene109 gene110 #> -0.0709498007 -0.8219652269 0.1480645195 2.9456916709 -0.0122949672 #> gene111 gene112 gene113 gene114 gene115 #> 0.2839370577 2.0544948698 1.1626483286 0.5053793788 0.2421696832 #> gene116 gene117 gene118 gene119 gene120 #> 0.0844107247 -0.0803013184 -0.5643669555 -1.7188430046 -0.0870387085 #> gene121 gene122 gene123 gene124 gene125 #> -0.7980706799 0.1763067762 -1.0104358820 -0.5043484459 -0.8508696070 #> gene126 gene127 gene128 gene129 gene130 #> -0.4504774952 0.0831771809 0.1292491327 -0.1079701896 -0.9943569067 #> gene131 gene132 gene133 gene134 gene135 #> 1.3826404211 -0.9152158633 0.3566664771 1.1007520297 -0.3313569211 #> gene136 gene137 gene138 gene139 gene140 #> 0.2902511729 0.3819533476 -0.4829485883 -0.1836136600 0.5848265961 #> gene141 gene142 gene143 gene144 gene145 #> -0.7516164933 0.0115963418 0.1017852364 -0.4912890991 -0.1845558255 #> gene146 gene147 gene148 gene149 gene150 #> -0.2219967606 0.1585005646 -0.3802636904 -0.5885573062 -0.4115767283 #> gene151 gene152 gene153 gene154 gene155 #> -0.0099764194 -0.2917020108 -0.4031625973 0.1065319651 3.1197567110 #> gene156 gene157 gene158 gene159 gene160 #> -0.1320299247 -0.2261490925 0.1351444158 -0.0702447068 -0.0247901562 #> gene161 gene162 gene163 gene164 gene165 #> -0.1741981203 -0.4681943806 0.5815107427 0.2924012595 -0.2507584978 #> gene166 gene167 gene168 gene169 gene170 #> 0.0594556387 -0.0832269792 -0.0962487170 -0.9773632455 1.4085227431 #> gene171 gene172 gene173 gene174 gene175 #> 0.1777955268 0.2944941419 -0.0617194432 -0.0280248217 0.3283323247 #> gene176 gene177 gene178 gene179 gene180 #> 0.0641623273 0.3988852297 -0.2398614102 -0.1370347362 -0.2759183528 #> gene181 gene182 gene183 gene184 gene185 #> 1.0221041920 -0.2893786396 -0.0967568222 -0.1675586694 1.7921365752 #> gene186 gene187 gene188 gene189 gene190 #> -0.1198040204 -0.1059813220 0.7403619469 -0.1471387643 -0.1548959113 #> gene191 gene192 gene193 gene194 gene195 #> -0.8463582529 -0.5388246104 -1.3156340055 0.7417535773 1.2138944247 #> gene196 gene197 gene198 gene199 gene200 #> -1.1079384610 0.0204635851 0.0479272083 0.1895427253 -0.3146934376 #> gene201 gene202 gene203 gene204 gene205 #> -0.3922634486 0.8106479422 -0.0229905338 0.0470393544 -0.2854608746 #> gene206 gene207 gene208 gene209 gene210 #> -0.6979760083 -0.0867551531 -1.9314930181 -0.9667665575 1.3723604915 #> gene211 gene212 gene213 gene214 gene215 #> -0.0896271182 0.7006349984 -0.0193539607 1.9862334539 -0.3252713486 #> gene216 gene217 gene218 gene219 gene220 #> 0.2964298274 -0.4028042447 0.0511856459 1.2764356751 0.9073659288 #> gene221 gene222 gene223 gene224 gene225 #> 0.7533420126 0.1600860043 0.0278880018 0.7117787538 -0.7395444984 #> gene226 gene227 gene228 gene229 gene230 #> 0.2136189237 0.3429540564 0.5444512699 0.3729581205 -1.1055078673 #> gene231 gene232 gene233 gene234 gene235 #> 0.2456387695 -6.7022193528 -0.8597032979 -0.3026552867 -0.4017424531 #> gene236 gene237 gene238 gene239 gene240 #> -0.0176484792 1.6883558728 -0.1672806231 -0.0725960446 1.1733813890 #> gene241 gene242 gene243 gene244 gene245 #> 0.7615544027 -0.8680982746 2.3723478523 -0.1774254408 -0.4059439893 #> gene246 gene247 gene248 gene249 gene250 #> -0.2656085629 -0.4635897928 1.4758045217 -0.0890749230 1.7212608298 #> gene251 gene252 gene253 gene254 gene255 #> -0.1453297058 0.0547650269 0.5232943656 -0.7011403312 -0.4677582008 #> gene256 gene257 gene258 gene259 gene260 #> -0.0468365070 1.6221563778 -0.0300761383 -0.9625221404 0.7914931813 #> gene261 gene262 gene263 gene264 gene265 #> 0.1765005315 -0.0689887734 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