这是什么样的R对象？ 矩阵列表，或矩阵矩阵或其他内容

Question

My colleague created this R object, but he does not work here any more.

I need to work with his R code, but I'm not able to figure out if the object he created is a List of matrices, or matrix of matrices or something else.

I did some queries on the object and a screen shot, hopefully this will give you an idea about the R object.

> dim(fmr.seg.crc)
[1] 10 22
> dimnames(fmr.seg.crc)
[[1]]
 [1] "s1"  "s2"  "s3"  "s4"  "s5"  "s6"  "s7"  "s8"  "s9"  "s10"

[[2]]
 [1] "1"  "2"  "3"  "4"  "5"  "6"  "7"  "8"  "9"  "10" "11" "12" "13" "14" "15" "16" "17" "18"
[19] "19" "20" "21" "22"
> head(fmr.seg.crc[[1]])
     start  end    value
[1,]     1  576 2.030296
[2,]   577 1112 1.945320
[3,]  1113 1511 1.929819
[4,]  1512 2113 1.868648
[5,]  2114 2573 1.938822
[6,]  2574 3992 1.966110

> fmr.seg.crc[1,2]
[[1]]
       start    end    value
 [1,]      1   1683 2.009863
 [2,]   1684   3683 1.943753
 [3,]   3684   7272 2.004721
 [4,]   7273   7823 1.909030
 [5,]   7824  12166 2.021245
 [6,]  12167  13125 1.909732
 [7,]  13126  15006 2.040557
 [8,]  15007  16044 1.965647
 [9,]  16045  16598 2.039992
[10,]  16599  17470 2.107079
[11,]  17471  17521 2.021539
[12,]  17522  18364 1.942838
[13,]  18365  19195 2.094474
[14,]  19196  21016 2.021019
[15,]  21017  22644 1.970473
[16,]  22645  23065 2.030463
[17,]  23066  23689 2.134962
[18,]  23690  23823 2.037685
[19,]  23824  28197 2.012424
[20,]  28198  33313 2.042131
[21,]  33314  35797 1.991916
[22,]  35798  35824 2.025841
[23,]  35825  37962 2.062941
[24,]  37963  41552 2.021660
[25,]  41553  46006 2.046230
[26,]  46007  50217 2.014589
[27,]  50218  51558 1.945273
[28,]  51559  57890 2.019592
[29,]  57891  58896 2.117450
[30,]  58897  59443 2.052708
[31,]  59444  59533 2.029076
[32,]  59534  62300 1.971623
[33,]  62301  64252 2.047004
[34,]  64253  66429 1.980032
[35,]  66430  70187 2.039259
[36,]  70188  72583 1.999711
[37,]  72584  74952 2.037337
[38,]  74953  75459 1.994685
[39,]  75460  76248 1.907432
[40,]  76249  77551 1.974716
[41,]  77552  82026 2.026742
[42,]  82027  83915 1.971480
[43,]  83916  87782 2.021381
[44,]  87783  90469 2.059347
[45,]  90470  91817 2.000065
[46,]  91818  93625 2.080138
[47,]  93626  94351 2.033229
[48,]  94352  97927 2.002070
[49,]  97928 107217 2.059019
[50,] 107218 115066 2.033657
[51,] 115067 118643 2.082806
[52,] 118644 123727 2.043857
[53,] 123728 125791 2.095192
[54,] 125792 126639 2.056129
[55,] 126640 129253 2.025997
[56,] 129254 132674 2.071402
[57,] 132675 133815 1.993041
[58,] 133816 136346 2.053994
[59,] 136347 136743 1.997972
[60,] 136744 139120 1.963982
[61,] 139121 140701 2.059231
[62,] 140702 142317 1.983171
[63,] 142318 147205 2.032126
[64,] 147206 149266 1.958569
[65,] 149267 151682 2.007082
[66,] 151683 153611 1.956822

Screen shot of the object in R looks like this:

My task is to convert a regular input file with 4 columns into this R object. My input data looks like this :

> head(seg2b)
     Chromosome     Start       End     value
[1,]          1     62920    462795 2.2251460
[2,]          1    462894  54574132 1.5044123
[3,]          1  54574878  54575365 0.2056125
[4,]          1  54576652 112147704 1.5074394
[5,]          1 112153343 112154768 2.4605827
[6,]          1 112163334 116601768 1.5106820

Answer 1

It is a matrix whose entries are lists consisting of one element, which is again a matrix. For instance,

m <- matrix(1:4, 2, 2)
(obj <- matrix(list(m, m, m, m), 2, 2))
#      [,1]      [,2]     
# [1,] Integer,4 Integer,4
# [2,] Integer,4 Integer,4

obj[1, 1]
# [[1]]
#      [,1] [,2]
# [1,]    1    3
# [2,]    2    4

Without further information it's not really clear what to do with your new input. Perhaps there is a separate submatrix for each new value of Chromosome . In your example you have only a single value of it, so then

(obj <- matrix(list(seg2b[, -1]), 1, 1))
#      [,1]  
# [1,] List,3

obj[1,1]
# [[1]]
#          Start       End     value
# [1,]     62920    462795 2.2251460
# [2,]    462894  54574132 1.5044123
# [3,]  54574878  54575365 0.2056125
# [4,]  54576652 112147704 1.5074394
# [5,] 112153343 112154768 2.4605827
# [6,] 112163334 116601768 1.5106820

But I guess in your full input data there are multiple Chromosome values. As to give a full answer, it is necessary to know what columns and rows of obj represent.