Using spread with duplicate identifiers for rows giving error

问题

My data looks like this:

df <- read.table(header = T, text =
        "GeneID    Gene_Name   Species    Paralogues    Domains   Functional_Diversity
         1234      DDR1        hsapiens   14            2         8.597482
         5678      CSNK1E      celegans   70            4         8.154788
         9104      FGF1        Chicken    3             0         5.455874
         4575      FGF1        hsapiens   4             6         6.745845")

I need it to look like:

   Gene_Name    hsapiens    celegans    ggalus
   DDR1         8.597482    NA          NA
   CSNK1E       NA          8.154788    NA
   FGF1         6.745845    NA          5.455874

I've tried using:

library(tidyverse)
df %>% 
    select(Gene_Name, Species, Functional_Diversity) %>% 
    spread(Species, Functional_Diversity)

My actual data consists of 130,000 rows (many Gene Names approx 14,000 unique), consisting of 9 species.

When I apply this method to my actual data I get:

Error: Duplicate identifiers for rows (16691, 19988), (20938, 21033), (1232, 21150), (2763, 21465), (1911, 20844), (17274, 17657, 18293, 18652, 18726, 19006, 19025), (496, 22555), (17227, 17608, 18211, 18605, 18676, 18967, 19002), (13569, 21807), (10261, 21014, 21607), (20816, 21553), (2244, 22025), (6194, 21910), (12217, 21555), (2936, 21078), (16484, 20911), (12216, 21851), (9289, 21791), (10340, 21752), (1714, 22077), (13216, 22618), (6076, 22371), (14731, 21717), (160, 22472), (11553, 22635), (17183, 17583, 18510, 18608, 18661, 18896, 19108), (138, 20028), (17185, 17584, 18330, 18415, 18500, 18981, 19063), (9726, 22440), (17238, 17617, 18905, 18960, 18996, 19134), (1638, 21645), (4631, 20821), (9162, 22463), (319, 20900), (13600, 22227), (9312, 20011), (14825, 21711, 21764), (3381, 21134), (505, 21133), (5954, 20013), (5948, 21313), (17233, 17612, 18187, 18311, 18411, 18708, 18980), (16953, 20902, 21845), (20710, 22477), (20519, 20973), (10204, 21197, 21213), (2933, 20707), (4302,

回答1:

To see just the rows that have "Duplicate identifiers", you could use...

df %>% 
  group_by(Gene_Name, Species) %>% 
  mutate(n = n()) %>% 
  filter(n > 1)

To ensure the spread works, even if you have rows with duplicate identifiers, you can add a row number column which will guarantee that each row is unique...

df %>% 
  select(Gene_Name, Species, Functional_Diversity) %>% 
  mutate(row = row_number()) %>% 
  spread(Species, Functional_Diversity)

来源：https://stackoverflow.com/questions/50259905/using-spread-with-duplicate-identifiers-for-rows-giving-error

标签

dataframe

tidyr

spread

biomart