DataFrame Construction With Non-standard Column
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Dario Strbenac ★ 1.5k
@dario-strbenac-5916
Last seen 9 days ago
Australia

Why does one fail but the other succeeds?

> DataFrame(ID = LETTERS[1:3], score = list(2:4, 6, 7:8))
Error in DataFrame(ID = LETTERS[1:3], score = list(2:4, 6, 7:8)) : 
  cannot coerce class "list" to a DataFrame
> data <- DataFrame(ID = LETTERS[1:3])
> data$score <- list(2:4, 6, 7:8)
> data
DataFrame with 3 rows and 2 columns
           ID  score
  <character> <list>
1           A  2,3,4
2           B      6
3           C    7,8
S4Vectors • 383 views
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@herve-pages-1542
Last seen 1 hour ago
Seattle, WA, United States

You need to protect the list by wrapping it in I(), otherwise the DataFrame() constructor interprets it as a list of 3 columns (so it tries to turn it into a DataFrame and fails because the columns don't have the same length):

library(S4Vectors)

DataFrame(ID = LETTERS[1:3], score = I(list(2:4, 6, 7:8)))
DataFrame with 3 rows and 2 columns
#            ID  score
#   <character> <list>
# 1           A  2,3,4
# 2           B      6
# 3           C    7,8

Note that this is no different from what happens with ordinary data frames:

data.frame(ID = LETTERS[1:3], score = list(2:4, 6, 7:8))
# Error in (function (..., row.names = NULL, check.rows = FALSE, check.names = TRUE,  : 
#   arguments imply differing number of rows: 3, 1, 2

data.frame(ID = LETTERS[1:3], score = I(list(2:4, 6, 7:8)))
#   ID   score
# 1  A 2, 3, 4
# 2  B       6
# 3  C    7, 8

If you don't protect, data.frame() and DataFrame() want to interpret the list as a list of columns (so 3 columns in this case):

data.frame(ID = LETTERS[1:3], score = list(A=2:4, B=letters[1:3], C=7:9))
#  ID score.A score.B score.C
# 1  A       2       a       7
# 2  B       3       b       8
# 3  C       4       c       9

DataFrame(ID = LETTERS[1:3], score = list(A=2:4, B=letters[1:3], C=7:9))
# DataFrame with 3 rows and 4 columns
#            ID   score.A     score.B   score.C
#   <character> <integer> <character> <integer>
# 1           A         2           a         7
# 2           B         3           b         8
# 3           C         4           c         9

Best,

H.

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Out of interest, SimpleList() works without I(), why is that?

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Same reason that list works without I. Both data.frame and DFrame objects have an expectation that the resulting object should have equal numbers of rows. A list or SimpleList can contain anything in each list item.

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suppressMessages(library(S4Vectors))

DataFrame(ID = LETTERS[1:3], score = list(2:4, 6, 7:8))
#> Error in DataFrame(ID = LETTERS[1:3], score = list(2:4, 6, 7:8)): cannot coerce class "list" to a DataFrame

DataFrame(ID = LETTERS[1:3], score = SimpleList(2:4, 6, 7:8))
#> DataFrame with 3 rows and 2 columns
#>            ID  score
#>   <character> <List>
#> 1           A  2,3,4
#> 2           B      6
#> 3           C    7,8
Created on 2023-09-25 by the reprex package (v2.0.1)
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2
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SimpleList is a List derivative and List derivatives in general don't need protection. For example, a GRangesList object (which is also a List derivative) does not need protection either:

library(GenomicRanges)

grl <- GRangesList(GRanges("chr1", IRanges(1, 4:6)),
                   GRanges(),
                   GRanges("chr2", IRanges(5, 9:8)))

is(grl, "List")
# [1] TRUE

DataFrame(ID = LETTERS[1:3], region=grl)
# DataFrame with 3 rows and 2 columns
#            ID                     region
#   <character>              <GRangesList>
# 1           A chr1:1-4,chr1:1-5,chr1:1-6
# 2           B                           
# 3           C          chr2:5-9,chr2:5-8
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Oh, ok. I understand. Technically both should work according to what the help page for DataFrame says (both SimpleList and list have [ and length functions and respect drop = FALSE). I don't know about the technicalities of the implementation, so maybe Herve will provide details.

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