R: how to expand a row containing a "list" to several rows...one for each list member?

Question

I am sure there is a simple solution to this, but i am going nuts trying to find it. Any help is very much appreciated.

I have a data frame with 2 columns; "pro" and "pep". pro is formatted as factors and contains entries in the form 220;300;4 sometimes more numbers (seperated by ";") and sometimes just a single number (and no ";"). The pep column is formatted as integers and contains single numbers, e.g. 20. What i would like to do is to "expand" e.g. the row pro: 220;300;4 and pep: 20 to three rows one with pro: 220 and pep: 20, one with pro: 300 and pep: 20 and one with pro: 4 and pep: 20.

I want to do this for the whole data frame and thus end up with a data frame with two character formatted columns where all the rows originally containing multiple ";" seperated numbers have been expanded.

I would prefer to avoid loops since the data frame is fairly large (>100000 rows)

I am sorry that i havent been able to post this in a more case-representative way...i am new here and got lost in the code format.

On a much appreciated request from simon:

    > dput( head( dat , 10 ) )
structure(list(Protein.Group.IDs = structure(c(1095L, 60L, 299L, 
242L, 1091L, 147L, 161L, 884L, 783L, 1040L), .Label = c("0", 
"1", "10", "100", "101", "102", "103", "104", "105", "106", "107", 
"108", "109", "11", "110", "111", "112", "113", "114", "114;680", 
"115", "116", "117", "118", "119", "12", "120", "121", "121;920;530", 
"121;920;530;589", "121;920;530;589;934", "121;920;589", "121;920;934", 
"122;351", "122;351;950", "122;351;950;224;904", "122;351;950;687", 
"122;901;224;904", "122;901;351", "122;901;351;950", "122;901;351;950;224", 
"122;901;351;950;224;890;904", "122;901;351;950;224;890;904;687", 
"122;901;351;950;890;687", "122;901;950", "122;901;950;904;687", 
"122;950", "123", "124", "125", "126", "127", "127;952", "128", 
"129", "13", "130", "131", "131;204", "132", "133", "134", "135", 
"136", "137", "138", "139", "14", "140", "140;259;436", "141", 
"142", "143", "144", "145", "146", "147", "148", "149", "15", 
"150", "151", "152", "153", "154", "155", "156", "157", "158", 
"159", "16", "16;331", "16;331;329", "16;331;329;62", "16;331;329;910", 
"16;331;329;910;62", "16;331;62", "16;331;910", "160", "161", 
"162", "163", "164", "165", "166", "166;743", "167", "167;595", 
"168", "169", "17", "170", "170;48", "171", "172", "173", "174", 
"175", "176", "177", "178", "179", "18", "180", "181", "182", 
"183", "184", "185", "186", "187", "188", "188;813", "188;813;852", 
"189", "19", "19;14", "19;6;9;14;11", "19;884;6;9;14;20;26;11;1", 
"19;9", "19;9;14", "190", "190;260", "191", "192", "193", "194", 
"195", "196", "197", "198", "199", "2", "20", "20;26", "200", 
"201", "202", "203", "204", "205", "206", "207", "208", "209", 
"21", "21;4", "210", "211", "212", "213", "214", "215", "216", 
"217", "218", "219", "22", "220", "221", "222", "223", "224", 
"224;890", "224;890;904", "225", "225;221", "225;221;308", "225;295", 
"226", "227", "228", "228;396", "228;396;73", "228;73", "229", 
"23", "23;137", "23;17;137", "230", "231", "232", "233", "234", 
"235", "236", "237", "238", "239", "24", "240", "241", "242", 
"242;171", "243", "244", "245", "246", "247", "248", "249", "25", 
"250", "251", "252", "253", "254", "255", "256", "257", "258", 
"259", "26", "260", "261", "262", "263", "264", "265", "266", 
"267", "268", "269", "27", "270", "271", "272", "273", "273;541;905", 
"273;905", "274", "275", "276", "277", "278", "279", "28", "280", 
"281", "281;192", "282", "283", "284", "285", "286", "287", "288", 
"289", "29", "290", "291", "292", "293", "294", "295", "296", 
"297", "298", "299", "3", "30", "300", "301", "302", "303", "304", 
"304;770", "305", "306", "307", "308", "309", "31", "310", "311", 
"312", "313;293", "314", "314;658", "315", "316", "317", "318", 
"319", "32", "320", "321", "322", "323", "324", "324;34;564;637;282;229;565", 
"324;564;282", "324;637;229;565", "325", "326", "327", "328", 
"328;586", "329", "33", "330", "331", "332", "333", "334", "335", 
"336", "337", "338", "339", "34", "340", "341", "342", "343", 
"344", "345", "346", "346;523", "347", "348", "349", "35", "350", 
"351", "351;890", "352", "353", "353;277", "354", "355", "356", 
"357", "358", "359", "36", "360", "361", "362", "363", "364", 
"365", "366", "367", "368", "369", "37", "370", "371", "372", 
"373", "374", "375", "376", "377", "377;938", "378", "379", "38", 
"380", "381", "382", "382;147", "383", "384", "385", "386", "387", 
"388", "389", "39", "39;417", "390", "391", "392", "393", "394", 
"395", "396", "397", "398", "399", "399;955", "4", "40", "400", 
"401", "402", "403", "404", "405", "406", "407", "408", "409", 
"41", "410", "411", "412", "413", "414", "415", "416", "417", 
"418", "419", "42", "420", "421", "422", "423", "424", "424;640", 
"425", "426", "427", "427;930", "428", "429", "43", "430", "431", 
"432", "433", "434", "435", "436", "437", "438", "438;178", "439", 
"44", "440", "441", "442", "443", "444", "445", "446", "447", 
"448", "449", "45", "450", "451", "452", "453", "454", "455", 
"456", "457", "458", "459", "46", "460", "461", "462", "463", 
"464", "465", "466", "467", "468", "469", "47", "470", "471", 
"472", "473", "474", "475", "476", "477", "478", "479", "48", 
"480", "481", "482", "483", "484", "485", "486", "487", "488", 
"488;648", "489", "49", "490", "491", "492", "493", "494", "495", 
"496", "497", "498", "499", "5", "50", "500", "501", "502", "503", 
"504", "505", "506", "507", "508", "509", "51", "510", "511", 
"512", "513", "514", "515", "516", "516;603;845", "516;603;845;837", 
"517", "518", "519", "52", "520", "521", "522", "523", "524", 
"525", "526", "527", "527;509", "528", "529", "53", "530", "531", 
"532", "533", "534", "535", "536", "537", "538", "539", "54", 
"540", "540;67", "541", "542", "543", "544", "545", "546", "547", 
"548", "549", "55", "550", "550;549", "551", "552", "553", "554", 
"555", "556", "557", "558", "559", "56", "560", "561", "562", 
"563", "564", "564;282", "564;637", "565", "566", "567", "568", 
"568;569", "568;569;286", "568;569;574", "568;569;574;286", "568;574", 
"569", "57", "570", "571", "572", "573", "574", "575", "576", 
"577", "578", "579", "579;577;578", "579;577;580", "579;577;580;578", 
"58", "580", "581", "582", "583", "584", "585", "585;609", "586", 
"587", "587;167", "587;167;595", "587;167;595;557", "588", "589", 
"59", "590", "591", "592", "593", "594", "595", "596", "597", 
"598", "599", "6", "60", "600", "601", "601;10", "602", "603", 
"604", "605", "606", "607", "608", "609", "61", "610", "611", 
"612", "613", "614", "615", "615;269", "615;926;269", "616", 
"617", "618", "619", "62", "620", "621", "622", "623", "624", 
"625", "626", "627", "628", "629", "63", "63;397", "630", "631", 
"632", "633", "634", "635", "636", "637", "638", "639", "64", 
"64;72", "640", "641", "642", "643", "643;529", "644", "645", 
"646", "647", "648", "649", "65", "650", "651", "652", "653", 
"654", "655", "656", "657", "658", "659", "66", "660", "661", 
"662", "663", "663;819", "664", "665", "666", "667", "668", "669", 
"67", "670", "671", "672", "673", "674", "675", "676", "677", 
"678", "679", "68", "680", "681", "681;97", "682", "683", "684", 
"685", "686", "687", "688", "689", "69", "690", "691", "692", 
"693", "694", "695", "696", "697", "698", "699", "7", "7;25;5", 
"7;752", "7;752;24", "7;752;25;24;8", "70", "700", "701", "702", 
"703", "704", "705", "706", "707", "708", "709", "71", "710", 
"711", "712", "713", "714", "715", "716", "717", "718", "719", 
"72", "72;746;944", "72;746;944;772", "72;772", "72;927", "720", 
"721", "722", "723", "724", "725", "726", "727", "728", "729", 
"73", "730", "731", "732", "733", "734", "735", "735;522", "735;665", 
"735;665;522", "735;665;876", "735;876", "735;876;522", "736", 
"737", "738", "739", "74", "740", "741", "742", "743", "744", 
"745", "746", "746;944", "746;944;772", "747", "748", "749", 
"75", "750", "751", "752", "752;24", "753", "754", "755", "756", 
"757", "758", "759", "76", "76;313", "76;313;293", "760", "761", 
"762", "763", "764", "765", "766", "767", "768", "769", "77", 
"770", "771", "772", "773", "774", "775", "776", "777", "778", 
"779", "78", "780", "781", "782", "783", "784", "785", "786", 
"787", "788", "789", "79", "790", "790;552", "791", "792", "793", 
"793;863", "794", "795", "796", "797", "798", "799", "8", "80", 
"800", "801", "802", "803", "804", "805", "806", "807", "808", 
"808;21", "809", "81", "810", "811", "812", "813", "814", "815", 
"815;413", "815;777", "815;777;339", "815;777;838", "815;838", 
"816", "817", "818", "818;7;752", "818;7;752;23;25;17;8", "819", 
"82", "820", "821", "822", "823", "824", "824;957", "825", "826", 
"827", "828", "829", "83", "830", "831", "832", "833", "834", 
"835", "836", "837", "838", "839", "84", "840", "841", "842", 
"843", "844", "845", "846", "847", "847;560;590", "848", "849", 
"85", "850", "850;817", "851", "852", "853", "853;420", "854", 
"855", "856", "857", "858", "858;638", "858;638;409", "859", 
"86", "860", "861", "861;593", "862", "863", "864", "865", "866", 
"867", "868", "869", "869;614", "87", "870", "871", "872", "873", 
"874", "875", "876", "877", "878", "879", "88", "880", "881", 
"882", "883", "884", "884;6", "884;6;9", "885", "886", "887", 
"888", "888;189", "889", "89", "890", "890;904", "891", "891;953", 
"892", "892;941", "893", "894", "895", "896", "897", "898", "899", 
"9", "90", "900", "901", "901;224", "902", "903", "904", "905", 
"906", "907", "908", "909", "91", "910", "911", "912", "913", 
"914", "915", "916", "917", "918", "918;947", "919", "92", "920;530;589", 
"920;530;589;934", "921", "922", "923", "924", "924;576", "925", 
"926", "927", "928", "929", "93", "930", "931", "932", "933", 
"934", "935", "936", "937", "938", "939", "94", "940", "941", 
"942", "943", "944", "945", "946", "947", "948", "949", "95", 
"950", "951", "952", "953", "954", "955", "956", "957", "958", 
"959", "96", "960", "961", "962", "963", "964", "965", "966", 
"967", "97", "98", "99", "99;392"), class = "factor"), Mod..Peptide.ID = c(23L, 
24L, 25L, 26L, 27L, 29L, 30L, 31L, 32L, 33L)), .Names = c("Protein.Group.IDs", 
"Mod..Peptide.ID"), row.names = c(318L, 344L, 380L, 406L, 409L, 
417L, 436L, 462L, 494L, 505L), class = "data.frame")

Kind Regards Mads

Answer 1

I've grown to really love data.table for this kind of task. It is so very simple. But first, let's make some sample data (which you should provide idealy!)

#  Sample data
set.seed(1)
df = data.frame( pep = replicate( 3 , paste( sample(999,3) , collapse=";") ) , pro = sample(3) , stringsAsFactors = FALSE )

Now we use the data.table package to do the reshaping in a couple of lines...

#  Load data.table package
require(data.table)

#  Turn data.frame into data.table, which looks like..
dt <- data.table(df)
#           pep pro
#1: 266;372;572   1
#2: 908;202;896   3
#3: 944;660;628   2

# Transform it in one line like this...
dt[ , list( pep = unlist( strsplit( pep , ";" ) ) ) , by = pro ]
#   pro pep
#1:   1 266
#2:   1 372
#3:   1 572
#4:   3 908
#5:   3 202
#6:   3 896
#7:   2 944
#8:   2 660
#9:   2 628

Answer 2

I think tidyr's unnest() is what you're looking for.

df <- tibble::tibble(x = 1:2, y = list(c("a", "b", "c"), c("alpha", "beta")))
df
#> # A tibble: 2 x 2
#>       x y        
#>   <int> <list>   
#> 1     1 <chr [3]>
#> 2     2 <chr [2]>
tidyr::unnest(df, cols = y)
#> # A tibble: 5 x 2
#>       x y    
#>   <int> <chr>
#> 1     1 a    
#> 2     1 b    
#> 3     1 c    
#> 4     2 alpha
#> 5     2 beta

^{Created on 2019-08-10 by the reprex package (v0.3.0)}

Answer 3

You have already obtained a nice answer, but it may be useful to dig around in the R toolbox. Here's an example using a function from the splitstackshape package, concat.split.multiple. As the name suggests it "allows the user to split multiple columns at once". Although there is only one concatenated column to split in the current example, the function is convenient because it allows us to reshape the data to a long format in the same call. Using the minimal data set provided by @SimonO101:

library(splitstackshape)
df2 <- concat.split.multiple(data = df, split.cols = "pep", seps = ";", direction = "long")
df2
#   pro time pep
# 1   1    1 236
# 2   3    1 465
# 3   2    1 641
# 4   1    2  16
# 5   3    2 721
# 6   2    2 323
# 7   1    3 912
# 8   3    3 459
# 9   2    3 283

An id variable ('time') is added to differentiate the multiple items ('pep') that is generated for each group ('pro'). If you wish to remove it, just run subset(df2, select = -time)