readr：デリミタをマージする必要がある場所を読むためのベストプラクティス？

Question

人間の読書を容易にするために、ファイル内のスペースが重複することがあります。しかし、読者のread_delimはこのユースケースを処理できません。 PLINKから

出力例：

FID   IID PHENO CNT CNT2 SCORE 
    0 ERR1136327  -9 2000 417 -0.000263553 
    0 ERR1136328  -9 2808 755 -0.000119435 
    0 ERR1136329  -9 1026 242 8.63494e-05 
    0 ERR1136330  -9 2688 880 0.000517726 
    0 ERR1136331  -9 1868 567 0.000264016 
    0 ERR1136332  -9 3522 1368 0.000144985 

（初期数行）

はread_delimを読んで試してみてください：

> d = read_delim("data/no_vcf_filtering/plink.profile", delim = " ") 
Missing column names filled in: 'X1' [1], 'X3' [3], 'X4' [4], 'X5' [5], 'X6' [6], 'X7' [7], 'X8' [8], 'X9' [9], 'X10' [10], 'X11' [11], 'X13' [13], 'X15' [15], 'X16' [16], 'X17' [17], 'X19' [19], 'X20' [20], 'X22' [22], 'X23' [23], 'X24' [24]Parsed with column specification: 
cols(
    .default = col_character(), 
    X4 = col_integer(), 
    IID = col_integer(), 
    X15 = col_integer(), 
    X16 = col_integer(), 
    X17 = col_integer(), 
    CNT = col_integer(), 
    X19 = col_double(), 
    X20 = col_double(), 
    CNT2 = col_double(), 
    X22 = col_double(), 
    X23 = col_double(), 
    X24 = col_double(), 
    SCORE = col_double() 
) 
See spec(...) for full column specifications. 
number of columns of result is not a multiple of vector length (arg 1)215 parsing failures. 
row # A tibble: 5 x 5 col  row col expected  actual         file expected <int> <chr>  <chr>  <chr>         <chr> actual 1  1 <NA> 25 columns 20 columns 'data/no_vcf_filtering/plink.profile' file 2  2 <NA> 25 columns 20 columns 'data/no_vcf_filtering/plink.profile' row 3  3 <NA> 25 columns 20 columns 'data/no_vcf_filtering/plink.profile' col 4  4 <NA> 25 columns 20 columns 'data/no_vcf_filtering/plink.profile' expected 5  5 <NA> 25 columns 20 columns 'data/no_vcf_filtering/plink.profile' 
... ................. ... ......................................................................... ........ ......................................................................... ...... ......................................................................... .... ......................................................................... ... ......................................................................... ... ......................................................................... ........ ......................................................................... 
See problems(...) for more details. 

ここで明らかな解決策は動作しません：

d = read_delim("data/no_vcf_filtering/plink.profile", delim = " +") 
Parsed with column specification: 
cols(
    .default = col_character(), 
    X4 = col_integer(), 
    IID = col_integer(), 
    X15 = col_integer(), 
    X16 = col_integer(), 
    X17 = col_integer(), 
#etc. 

スペースをタブに変換し、改行と結びつけてからtsvとして読んで（この場合は最初の空の列を取り除く）、丸ごとの解決策を見つけましたが、これは難しいことではありません。私は明白な何かを欠いていますか

> read_lines("data/no_vcf_filtering/plink.profile") %>% str_replace_all(" +", "\t") %>% str_c(collapse = "\n") %>% read_tsv() %>% .[, -1] 
# A tibble: 230 x 6 
    FID  IID PHENO CNT CNT2  SCORE 
    <int>  <chr> <int> <int> <int>  <dbl> 
1  0 ERR1136327 -9 2000 417 -2.63553e-04 
2  0 ERR1136328 -9 2808 755 -1.19435e-04 
3  0 ERR1136329 -9 1026 242 8.63494e-05 
4  0 ERR1136330 -9 2688 880 5.17726e-04 
5  0 ERR1136331 -9 1868 567 2.64016e-04 
6  0 ERR1136332 -9 3522 1368 1.44985e-04 
7  0 ERR1136333 -9 870 110 -1.25087e-04 
8  0 ERR1136334 -9 2936 877 -6.35191e-04 
9  0 ERR1136335 -9 3048 914 -2.22427e-06 
10  0 ERR1136336 -9 3184 814 2.77346e-04 
# ... with 220 more rows 
Warning message: 
Missing column names filled in: 'X1' [1] 

Answer 1

readr::read_tableは、この形式に適した機能です。

> read_table("test.txt") 
Parsed with column specification: 
cols(
    FID = col_integer(), 
    IID = col_character(), 
    PHENO = col_integer(), 
    CNT = col_integer(), 
    CNT2 = col_integer(), 
    SCORE = col_double() 
) 
# A tibble: 6 x 6 
    FID  IID PHENO CNT CNT2  SCORE 
    <int>  <chr> <int> <int> <int>  <dbl> 
1  0 ERR1136327 -9 2000 417 -2.63553e-04 
2  0 ERR1136328 -9 2808 755 -1.19435e-04 
3  0 ERR1136329 -9 1026 242 8.63494e-05 
4  0 ERR1136330 -9 2688 880 5.17726e-04 
5  0 ERR1136331 -9 1868 567 2.64016e-04 
6  0 ERR1136332 -9 3522 1368 1.44985e-04 

これもbase::機能の真である - read.table対read.delim。