Comparaison de fichier

**Aline Davaud** · 29/01/2021, 12h01

Bonjour,

Je démarre en r, et j'aimerai comparer deux fichier.

-> gene_splite: tableau de 986 ligne et 14 colonnes. La 1ere colonne contient toujours un gène. Les colonne 2 a 14 contiennent soit un gène, soit sont vides
-> gene_list: vecteur contenant une liste de gènes

Je souhaiterai ajouter une colonne dans gene_splite qui indiquerait si la ligne de ce tableau contient un gène qu'on peut retrouver dans gene_list.
J'ai fait plusieurs tentative, mais les résultats ne correspondent pas à ma vérification manuelle sur les premières lignes. Pourriez vous m'aider à voir où se situe le problème

Voici à quoi ressemble gene_splite

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 [,1]             [,2]                 [,3]              [,4]             [,5]             [,6]               [,7]            [,8]         [,9]     [,10]    [,11]    [,12]   
  [1,] "TPOJSF18"       ""                   ""                ""               ""               ""                 ""              ""           ""       ""       ""       ""      
  [2,] "MLI4"           "B3AZVT6"            ""                ""               ""               ""                 ""              ""           ""       ""       ""       ""      
  [3,] "POJU2"          ""                   ""                ""               ""               ""                 ""              ""           ""       ""       ""       ""      
  [4,] "POJU2"          "PAZK4"              ""                ""               ""               ""                 ""              ""           ""       ""       ""       ""      
  [5,] "SPM45B1"        ""                   ""                ""               ""               ""                 ""              ""           ""       ""       ""       ""      
  [6,] "UPO4B"          ""                   ""                ""               ""               ""                 ""              ""           ""       ""       ""       ""      
  [7,] "CTUY6"          "MNUFR"              ""                ""               ""               ""                 ""              ""           ""       ""       ""       ""

Voici à quoi ressemble gene_list

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 [1] "ABS1"      "ABST"       "ABCZ2"      "AJPB7"      "ASDC9"      "ABSD"      "AB4"      "ABJK5"      "POK9"      "THIO"      "LOKL"      "UTRC"       "OTRA"

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for (i in 1:nrow(gene_splite)){
 for (j in 1:ncol(gene_splite)){
   for (k in gene_list){
     if (gene_splite[i,j] == k)
    {
     gene_splite$Present[i] ="yes"
     }
 
  }}}

Désolé, si mon message n'est pas bien formaté, je ne savais pas comment faire.
N'hésitez pas à me demander plus d'information pour pouvoir m'aider

Merci d'avance,

Aline

**olivier.decourt** · 29/01/2021, 16h02

Bonjour Aline.
Apparemment tes données de départ, gene_splite, sont dans une matrice (je suppose vu l'affichage) plutôt qu'un data.frame. Pas de souci.
On peut tout simplement poser la question à R que gene_splite %in% gene_list : ça renvoie TRUE ou FALSE pour chaque élément de la matrice gene_splite. On a juste à stocker le résultat dans une autre matrice.
Et si tu as besoin de sortir des stats par ligne ou colonne tu pourras utiliser des sum sur cette matrice via la fonction apply.

Par contre, quand tu proposes un exemple (je dis ça pour de futures questions) : 1) essaye de fournir un moyen de créer tes données ; 2) essaye que ton exemple soit facile à comprendre (ici il n'y avait aucun gène en commun entre la liste et la matrice... Je me suis permis d'en ajouter à la fin de gene_list).

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gene_split <- t(matrix(c ("TPOJSF18"  ,     ""            ,       ""      ,          ""     ,          ""       ,        ""         ,        ""         ,     ""      ,     ""      , ""      , ""    ,   "",      
                      "MLI4"          , "B3AZVT6" ,           ""  ,              "" ,              ""   ,            ""     ,            ""     ,         ""  ,         ""  ,     ""  ,     "",       "",      
                      "POJU2"       ,   ""              ,     ""        ,        ""       ,        ""         ,      ""           ,      ""           ,   ""        ,   ""       ,""       ,""      , "",      
                      "POJU2"       ,   "PAZK4"   ,           ""  ,              "" ,              ""   ,            ""     ,            ""     ,         ""  ,         ""  ,     ""  ,     "",       "",      
                      "SPM45B1"   ,     ""            ,       ""      ,          ""     ,          ""       ,        ""         ,        ""         ,     ""      ,     ""      , ""      , ""    ,   "",      
                      "UPO4B"       ,   ""              ,     ""        ,        ""       ,        ""         ,      ""           ,      ""           ,   ""        ,   ""       ,""       ,""      , "",      
                      "CTUY6"       ,   "MNUFR"   ,           ""  ,              "" ,              ""   ,            ""     ,            ""     ,         ""  ,         ""  ,     ""  ,     "",       ""),
                     ncol=7, nrow=12))
gene_list <- c("ABS1",
               "ABST",
               "ABCZ2",
               "AJPB7",
               "ASDC9",
               "ABSD",
               "AB4",
               "ABJK5",
               "POK9",
               "THIO",
               "LOKL",
               "UTRC",
               "OTRA",
               "PAZK4",
               "POJU2")
 
ok <- matrix(gene_split %in% gene_list,
                ncol=ncol(gene_split),
                nrow=nrow(gene_split))
 
# nombre de correspondances par ligne
apply(ok, FUN=sum, MARGIN=1)
 
# nombre de correspondances par colonne
apply(ok, FUN=sum, MARGIN=2)

**Aline Davaud** · 29/01/2021, 16h56

Bonjour,

Merci beaucoup pour votre méthode. J'ai réussi à rajouter ma colonne dans mon fichier et il me semble qu'il n'y a plus d'erreur.

Par contre, j'ai dû modifier un peu ma commande pour rajouter ma colonne car malgré votre méthode, je retombais exactement sur les même résultats qu'avec ma première tentative en solo. J'ai pu plus facilement adapter votre méthode pour rajouter ma colonne et maintenant ça m'a l'air ok.

En gros en appliquant votre commande

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 Count=apply(ok, FUN=sum, MARGIN=1)

j'obtenais ce vector

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 [1] 0 1 0 0 1 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
 [89] 1 0 0 0 0 0 0 1 0 0 0 0 1 1 0 0 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0
[177] 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 1 0 0 0 0 0
[265] 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 1 0
[353] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0
[441] 1 1 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
[529] 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 1 0 0 0 0
[617] 0 0 0 1 1 1 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 0 0 0 1 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 1 0 0 0 0 0 0 1 0 0 0
[705] 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 1 1 1 0
[793] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
[881] 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0
[969] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0

Mais quand j'essayais de créer ma colonne j'obtenais cette colonne

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 fichier$Present
  [1] NA    "yes" NA    "yes" "yes" "yes" "yes" "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" "yes" "yes" NA    "yes" NA   
 [30] "yes" "yes" "yes" "yes" "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes"
 [59] NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" "yes" "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA   
 [88] "yes" "yes" "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" "yes" "yes" NA    "yes" NA    "yes" "yes" "yes" NA    "yes" "yes" "yes" NA    "yes" NA    "yes"
[117] NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" "yes" "yes" "yes" "yes" "yes" "yes" NA    "yes" NA    "yes" NA    "yes" "yes" "yes" NA    "yes" NA    "yes" NA   
[146] "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" "yes" "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes"
[175] NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" "yes" "yes" "yes" "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA   
[204] "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes"
[233] NA    "yes" NA    "yes" NA    "yes" "yes" "yes" "yes" "yes" "yes" "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" "yes" "yes" NA    "yes" "yes" "yes" NA   
[262] "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes"
[291] NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" "yes" "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" "yes" "yes" NA    "yes" NA   
[320] "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" "yes" "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes"
[349] NA    "yes" "yes" "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA   
[378] "yes" NA    "yes" NA    "yes" "yes" "yes" NA    "yes" NA    "yes" "yes" "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes"
[407] NA    "yes" "yes" "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" "yes" "yes" NA   
[436] "yes" NA    "yes" NA    "yes" "yes" "yes" NA    "yes" NA    "yes" "yes" "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes"
[465] NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" "yes" "yes" "yes" "yes" NA    "yes" NA    "yes" "yes" "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA   
[494] "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" "yes" "yes" NA    "yes" NA    "yes" "yes" "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes"
[523] NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" "yes" "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA   
[552] "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes"
[581] "yes" "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" "yes" "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" "yes" "yes" NA    "yes" "yes"
[610] "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" "yes" "yes" NA    "yes" "yes" "yes" NA    "yes" NA    "yes" "yes" "yes" NA    "yes" NA    "yes" NA    "yes"
[639] NA    "yes" NA    "yes" NA    "yes" "yes" "yes" NA    "yes" NA    "yes" "yes" "yes" NA    "yes" "yes" "yes" "yes" "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" "yes"
[668] "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" "yes" "yes" NA    "yes" NA    "yes" NA    "yes"
[697] NA    "yes" NA    "yes" "yes" "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" "yes" "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" "yes" "yes" NA    "yes" NA   
[726] "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" "yes" "yes" NA    "yes" "yes" "yes" NA    "yes" NA    "yes"
[755] NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA   
[784] "yes" NA    "yes" "yes" "yes" "yes" "yes" "yes" "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" "yes" "yes"
[813] "yes" "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" "yes" "yes" NA    "yes" NA    "yes" NA    "yes" NA   
[842] "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" "yes" "yes" NA    "yes" "yes" "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" "yes" "yes"
[871] NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" "yes" "yes" NA    "yes" NA    "yes" NA    "yes" NA   
[900] "yes" "yes" "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" "yes" "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes"
[929] NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" "yes" "yes" "yes" "yes" "yes" "yes" "yes" "yes" NA    "yes" NA    "yes" NA    "yes" NA   
[958] "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" "yes" "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" NA    "yes" "yes" "yes" NA    "yes"

Ce qui n'allait pas rien qu'à la 5ieme ligne et ce qui équivaut exactement à ce que j'obtenais avant de poster ma demande.

J'ai réussi en utilisant une boucle for avec un if et un if not au lieu d'utiliser juste un if comme dans ma première tentative.

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  for (i in 1:length(Count)){
    if (Count[i]==1){
   fichier$Present[i]="Yes"}
    if (Count[i]==0){
      fichier$Present[i]="no"
    }
  }

Encore merci pour votre aide.

Aline

Comparaison de fichier

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