I want to add a Indication column in dat dataframe with the variables that correspond to the Profile column of the ann dataframe. The Indication column will have either 0/1 or 1/2 binary categorical variables for Unaffected control or BP variables, respectively.
library(dplyr)
phenocov <- dat %>% inner_join(ann %>% select("Database_ID", "Profile") %>% dummycov$PHENOTYPE==encode_binary(ann$Profile), by=c("FID"="Database_ID"))
Expected output
| FID | IID | SOL | C1 | C2 | Indication |
|---|---|---|---|---|---|
| AC13 | 1 | 0 | -0.02851720 | 0.00450319 | 1/2 |
| AC14 | 1 | 0 | -0.04220610 | 0.00394058 | 1/2 |
| AC15 | 1 | 0 | -0.01351050 | -0.03165270 | 0/1 |
dat dataframe
> dput(dat)
structure(list(FID = c("AC13", "AC14", "AC15", "AC18", "AC19",
"AC1", "AC20", "AC21", "AC23", "AC24", "AC27", "AC29", "AC2",
"AC30", "AC32", "AC33", "AC34", "AC35", "AC36", "AC38", "AC42",
"AC43", "AC46", "AC48", "AC49", "AC50", "AC51", "AC52", "AC53",
"AC54", "AC56", "AC57", "AC58", "AC5", "AC60", "AC61", "AC62",
"AC63", "AC64", "AC65", "AC67", "AC69", "AC6", "AC70", "AC71",
"AC72", "AC74", "AC76", "AC77", "AC79", "AC80", "AC83", "AC84",
"AC86", "AC89", "AC8", "AC90", "AC91", "AC102", "AC103", "AC104",
"AC105", "AC16", "AC95", "AC96", "AC99", "DE10", "DE12", "DE13",
"DE14", "DE16", "DE17", "DE22", "DE23", "DE27", "DE36", "DE37",
"DE38", "DE39", "DE3", "DE40", "DE45", "DE46", "DE47", "DE4",
"DE50", "DE51", "DE52", "DE55", "DE57", "DE59", "DE7", "DE32",
"DE43"), IID = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L), SOL = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L), C1 = c(-0.0285172, -0.0422061, -0.0135105, 0.0335788,
0.00453814, -0.0196805, 0.00871406, -0.0359998, 0.00776039, -0.0152431,
-0.0157209, 0.0235421, -0.0292564, 0.000164687, -0.0104566, -0.0078923,
-0.011623, 0.0173727, 0.00327281, -0.0101589, -0.00564814, 0.0232102,
0.00209183, -0.0245178, 0.0295213, -0.0012923, 0.00775297, 0.019803,
0.00521905, 0.0143496, 0.0243968, 0.0403667, 0.0420627, -0.0234294,
-0.00923894, 0.00216892, -0.0174861, 0.000902948, 0.0250136,
0.131506, 0.036772, -0.0314508, 0.0014534, 0.0123288, 0.0152248,
0.030759, 0.029896, 0.0257204, -0.0132957, -0.00942661, 0.0286468,
0.0297961, -0.0225471, 0.0185018, -0.0103523, -0.00141674, -0.00553813,
0.0141762, 0.0254432, -0.0124213, -0.0220576, 0.0278842, 0.00114805,
-0.013759, 0.00493565, -0.0146888, -0.00463272, -0.0332577, -0.0200095,
0.00230828, -0.0232427, 0.00433733, -0.0244282, -0.0245909, 0.0155191,
0.00425367, 0.00868522, -0.0347233, 0.00191488, -0.0154211, 0.0154046,
-0.00126067, 0.00826277, -0.0124104, -0.0136281, -0.023651, 0.00853699,
-0.0373163, 0.0147421, -0.0425991, -0.0198727, -0.0197213, -0.0115728,
-0.0127898), C2 = c(0.00450319, 0.00394058, -0.0316527, 0.00310475,
0.016075, 0.0108606, 0.0195024, -0.0109932, 0.02644, 0.00177053,
-0.0180791, -0.0128455, -0.0353571, 0.00868615, 0.0278649, -0.0143205,
0.0198699, 0.00600335, 0.00636933, -0.0245385, 0.0247255, -0.0019047,
0.00418658, -0.0106317, 0.0329249, -0.0490193, -0.0322256, -0.00525161,
0.0127281, -0.0210357, 0.048556, -0.0157994, 0.0225328, 0.0420733,
-0.0722942, 0.0117474, -0.00108231, -0.053874, -0.0351118, 0.000781904,
-0.0188162, -0.0214653, 0.0150199, 0.0339645, -0.0335628, -0.0151206,
0.0163763, -0.015727, -0.0232298, 0.0172519, 0.0348876, -0.026288,
0.0383726, -0.018123, 0.0200251, -0.0246757, 0.0184051, 0.0249351,
-0.00324928, 0.0129067, -0.0143993, -0.00150337, -0.00089652,
-0.0477761, 0.00873251, -0.0184572, 0.00115896, 0.0252723, -0.0188119,
0.0403222, -0.00957213, -0.0280059, 0.0183744, -0.025548, 0.021987,
0.0268481, -0.0267149, 0.00712551, -0.0115199, 0.00559716, 0.00779719,
-0.0181187, -0.0182654, -0.0263084, 0.00126466, 0.0397802, 0.0457278,
0.0098323, -0.00865206, 0.0248558, -0.0163334, 0.00451314, 0.0337946,
0.0267819)), class = "data.frame", row.names = c(NA, -94L))
The Database_ID and Profile columns in the ann dataframe (there are other columns in the ann dataframe...refer to below)
> dput(ann[c("Database_ID","Profile")])
structure(list(Database_ID = c("AC10", "AC11", "AC12", "AC13",
"AC14", "AC15", "AC17", "AC18", "AC19", "AC1", "AC20", "AC21",
"AC22", "AC23", "AC24", "AC25", "AC26", "AC27", "AC29", "AC2",
"AC30", "AC31", "AC32", "AC33", "AC34", "AC35", "AC36", "AC37",
"AC38", "AC39", "AC3", "AC40", "AC41", "AC42", "AC43", "AC45",
"AC46", "AC47", "AC48", "AC49", "AC50", "AC51", "AC52", "AC53",
"AC54", "AC55", "AC56", "AC57", "AC58", "AC5", "AC60", "AC61",
"AC62", "AC63", "AC64", "AC65", "AC66", "AC67", "AC69", "AC6",
"AC70", "AC71", "AC72", "AC73", "AC74", "AC75", "AC76", "AC77",
"AC78", "AC79", "AC7", "AC80", "AC81", "AC82", "AC83", "AC84",
"AC86", "AC87", "AC88", "AC89", "AC8", "AC90", "AC91", "AC92",
"AC9", "AC100", "AC101", "AC102", "AC103", "AC104", "AC105",
"AC16", "AC68", "AC93", "AC94", "AC95", "AC96", "AC97", "AC99",
"DE10", "DE12", "DE13", "DE14", "DE15", "DE16", "DE17", "DE18",
"DE19", "DE1", "DE20", "DE21", "DE22", "DE23", "DE25", "DE26",
"DE27", "DE2", "DE33", "DE34", "DE35", "DE36", "DE37", "DE38",
"DE39", "DE3", "DE40", "DE41", "DE42", "DE44", "DE45", "DE46",
"DE47", "DE48", "DE49", "DE4", "DE50", "DE51", "DE52", "DE53",
"DE54", "DE55", "DE56", "DE57", "DE58", "DE59", "DE60", "DE7",
"DE9", "DE29", "DE30", "DE32", "DE43", "DE5"), Profile = c("Schiz.",
"Schiz.", "Schiz.", "BP", "BP", "Unaffected control", "Schiz.",
"BP", "Unaffected control", "BP", "BP", "BP", "Schiz.", "BP",
"Unaffected control", "Schiz.", "Schiz.", "Unaffected control",
"Unaffected control", "BP", "Unaffected control", "Schiz.", "BP",
"Unaffected control", "BP", "Unaffected control", "BP", "Schiz.",
"Unaffected control", "Schiz.", "Schiz.", "Schiz.", "Schiz.",
"BP", "Unaffected control", "Schiz.", "BP", "Schiz.", "BP", "Unaffected control",
"BP", "Unaffected control", "Unaffected control", "Unaffected control",
"Unaffected control", "Schiz.", "Unaffected control", "BP", "BP",
"BP", "Unaffected control", "BP", "BP", "BP", "BP", "Unaffected control",
"Schiz.", "Unaffected control", "BP", "BP", "Unaffected control",
"Unaffected control", "BP", "Schiz.", "BP", "Schiz.", "BP", "Unaffected control",
"Schiz.", "Unaffected control", "Schiz.", "Unaffected control",
"Schiz.", "Schiz.", "Unaffected control", "Unaffected control",
"Unaffected control", "Schiz.", "Schiz.", "BP", "BP", "Unaffected control",
"Unaffected control", "Schiz.", "Schiz.", "Schiz.", "Schiz.",
"BP", "Unaffected control", "BP", "Unaffected control", "BP",
"Schiz.", "Schiz.", "Schiz.", "Unaffected control", "Unaffected control",
"Schiz.", "Unaffected control", "Unaffected control", "Unaffected control",
"BP", "BP", "Dep.", "Unaffected control", "Unaffected control",
"Dep.", "Dep.", "Dep.", "Dep.", "Dep.", "Unaffected control",
"Unaffected control", "Schiz.", "Dep.", "BP", "Dep.", "Schiz.",
"Schiz.", "Schiz.", "BP", "Unaffected control", "Unaffected control",
"Unaffected control", "BP", "BP", "Dep.", "Schiz.", "Dep.", "BP",
"Unaffected control", "Unaffected control", "Schiz.", "Schiz.",
"Unaffected control", "Unaffected control", "BP", "BP", "Schiz.",
"Dep.", "BP", "Dep.", "BP", "Schiz.", "Unaffected control", "Dep.",
"BP", "Schiz.", "Dep.", "Dep.", "BP", "BP", "Schiz.")), row.names = c("1",
"2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13",
"14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24",
"25", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35",
"36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46",
"47", "48", "49", "50", "51", "52", "53", "54", "55", "56", "57",
"58", "59", "60", "61", "62", "63", "64", "65", "66", "67", "68",
"69", "70", "71", "72", "73", "74", "75", "76", "77", "78", "79",
"80", "81", "82", "83", "84", "85", "86", "87", "88", "89", "90",
"91", "92", "93", "94", "95", "96", "97", "98", "99", "100",
"101", "102", "103", "104", "105", "106", "107", "108", "109",
"110", "111", "112", "113", "114", "115", "116", "117", "118",
"119", "120", "121", "122", "123", "124", "125", "126", "127",
"128", "129", "130", "131", "132", "133", "134", "135", "136",
"137", "138", "139", "140", "141", "142", "143", "144", "145",
"146", "147", "148", "149", "150", "151", "152", "153"), class = "data.frame")
There are other columns in ann, which I don't need.
> dput(head(ann))
structure(list(Database_ID = c("AC10", "AC11", "AC12", "AC13",
"AC14", "AC15"), Collection_type = c("Array", "Array", "Array",
"Array", "Array", "Array"), Age = c(40L, 51L, 19L, 49L, 48L,
44L), Round_Age = c(40L, 50L, 20L, 50L, 50L, 45L), sex = c("M",
"M", "M", "F", "F", "F"), race = c("White", "White", "White",
"White", "White", "White"), Profile = c("Schiz.", "Schiz.", "Schiz.",
"BP", "BP", "Unaffected control"), DSM_IV = c(295.9, 295.9, 295.9,
296.44, 296.7, NA), Axis_I_Primary_Dx = c("SCHIZ UNDIFF", "SCHIZ UNDIFF",
"SCHIZ UNDIFF", "BP I", "BP I", "CONTROL"), PMI = c(34L, 43L,
28L, 19L, 18L, 28L), Brain_PH = c(6.18, 6.63, 6.73, 5.87, 6.5,
6.59), Left_Brain = c("Fixed", "Frozen", "Frozen", "Fixed", "Frozen",
"Fixed"), Suicide_Status = c("No", "No", "No", "Yes", "No", "No"
), Psychotic_Feature = c("Yes", "Yes", "Yes", "Yes", "Unknown",
"No"), Rate_Of_Death = c("Possible anoxia at death (e.g., CO poisoning or pneumonia)",
"Sudden", "Sudden", "Sudden", "Sudden", "Sudden"), Exacerbation = c("No evidence of exacerbation",
"No evidence of exacerbation", "No evidence of exacerbation",
"Definite", "No evidence of exacerbation", "Unknown"), Smoking_At_TOD = c("Yes",
"Yes", "No", "Yes", "Yes", "Unknown"), Lifetime_Alcohol_Use = c("Moderate drinking in present (same as above, for recent period)",
"Moderate drinking in present (same as above, for recent period)",
"Social (1?2 drinks/day)", "Little or none (less than 1 drink/day)",
"Social (1?2 drinks/day)", "Moderate drinking in present (same as above, for recent period)"
), Lifetime_Drug_Use = c("Moderate drug use in present", "Social",
"Heavy drug use in present", "Little or none", "Moderate drug use in present",
"Little or none"), Lifetime_Antipsychotics = c(75000L, 130000L,
2500L, 4000L, 0L, 0L)), row.names = c("1", "2", "3", "4", "5",
"6"), class = "data.frame")