Error in `[[<-`(`*tmp*`, i, value = sub("\\_.*", "", i)) : attempt to select more than one element in vectorIndex

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英文:

Error in `[[<-`(`*tmp*`, i, value = sub("\\_.*", "", i)) : attempt to select more than one element in vectorIndex

问题

The Sample.ID column in the sample.sheet dataframe corresponds to the clin.info dataframe and may be duplicated. The File.Name column of the sample.sheet dataframe contains a substring that is extracted as basename. Only duplicate basename prefixes are retained for further analyses.

First, I find the rows of sample.sheet and clin.info with common Sample.ID information.

  1. sample.sheet <- sample.sheet[sample.sheet$Sample.ID %in% clin.info$Sample.ID, ]
  2. clin.info <- clin.info[clin.info$Sample.ID %in% sample.sheet$Sample.ID, ]

Then, I remove the substring and retain only samples with duplicate prefixes.

  1. rgx_undsc <- paste0(
  2.   "_[^_]*$"
  3. )
  5. basename <- sample.sheet %>%
  6.   # Add a column with everything (the prefix) before the "_" (the suffix).
  7.   mutate(file_prefix = str_remove(File.Name, rgx_undsc)) %>%
  8.   # Count the occurrences of each prefix.
  9.   group_by(file_prefix) %>%
  10.   summarize(n = n()) %>%
  11.   ungroup() %>%
  12.   # Include only those prefixes with multiple occurrences: duplicates.
  13.   filter(n > 1) %>%
  14.   select(file_prefix)

If Sample.ID has more than one pair, take the first pair.

  1. for(i in sample.sheet %>% group_by(Sample.ID) %>% filter(n() > 2)){
  2.   # Get the pairs
  3.   pairs[[i]] <- sub("\\_.*", "", i)
  4.   basename <- cbind(basename, pairs[[1]])
  5. }

Traceback:

  1. Error in `[[<-`(`*tmp*`, i, value = sub("\\_.*", "", i)) : 
  2.   attempt to select more than one element in vectorIndex

Data:

Example:

  1. > dput(sample.sheet)
  2. structure(list(File.Name = c("9d797850-f4e8-4799-8e36-f9611ce9ef99_noid_Red.idat", 
  3. "fdd60aca-ac18-43c0-b191-94fca93fb0b4_noid_Grn.idat", "fdd60aca-ac18-43c0-b191-94fca93fb0b4_noid_Red.idat", 
  4. "4086487a-70af-4091-8691-a04adbdefd94_noid_Red.idat", "9514c72b-27c9-4bff-bb8c-4cd809ab99cf_noid_Grn.idat", 
  5. "9514c72b-27c9-4bff-bb8c-4cd809ab99cf_noid_Red.idat", "ca04f909-7afa-4feb-b160-ae0e363e2004_noid_Grn.idat", 
  6. "295b1e9d-315d-4f87-8a86-38a9c2264f00_noid_Grn.idat", "6cab56c6-d37b-4bb2-b575-c0c924fe312d_noid_Grn.idat", 
  7. "71578b77-2494-4d65-8187-809a9277eb2f_noid_Grn.idat", "182cce6f-eb18-4c51-9c8d-47a0770ef79d_noid_Grn.idat", 
  8. "19d2e9e5-796e-4df5-96aa-68f5d0fa1855_noid_Grn.idat", "7dc90b83-0171-4600-883a-8de97c0e57cc_noid_Grn.idat", 
  9. "a3b85dd8-5621-4665-bafd-7edcf7c05aa4_noid_Red.idat", "b53495eb-ca7a-455b-b45c-338ef3689ca2_noid_Grn.idat", 
  10. "69df812d-f5cc-4c1d-ac76-01530e7df677_noid_Red.idat", "69df812d-f5cc-4c1d-ac76-01530e7df677_noid_Grn.idat", 
  11. "5723e331-d8e6-4687-ba89-3c0e9a8c9317_noid_Grn.idat", "6445036e-69bf-4f60-a1c1-b2506e32e53c_noid_Red.idat", 
  12. "c65756c7-7ef4-4c90-ac3a-15cacf6fa83e_noid_Red.idat", "4d87a92b-998b-4af6-a45b-a1cc95719597_noid_Grn.idat", 
  13. "e26a7836-17af-4498-8d69-
  15. <details>
  16. <summary>英文:</summary>
  18. The `Sample.ID` column in the `sample.sheet` dataframe correspond with that in `clin.info` dataframe and may be duplicated. The `File.Name` column of the `sample.sheet` dataframe contains a substring which is extracted as `basename`. Only duplicate `basename` prefixes are retained for further analyses.
  21. First, I find the rows of `sample.sheet` and `clin.info` with common `Sample.ID` info.
  23.     sample.sheet &lt;- sample.sheet[sample.sheet$Sample.ID %in% clin.info$Sample.ID, ]
  24.     clin.info &lt;- clin.info[clin.info$Sample.ID %in% sample.sheet$Sample.ID, ]
  26. Then, I remove the substring and retain only samples with duplicate prefix.
  27.     
  28.     rgx_undsc &lt;- paste0(
  29.       &quot;_[^_]*$&quot;
  30.     )
  31.     
  32.     basename &lt;- sample.sheet %&gt;%
  33.       # Add a column with everything (the prefix) before the &quot;_&quot; (the suffix).
  34.       mutate(file_prefix = str_remove(File.Name, rgx_undsc)) %&gt;%
  35.       # Count the occurrences of each prefix.
  36.       group_by(file_prefix) %&gt;%
  37.       summarize(n = n()) %&gt;%
  38.       ungroup() %&gt;%
  39.       # Include only those prefixes with multiple occurrences: duplicates.
  40.       filter(n &gt; 1) %&gt;%
  41.       select(file_prefix) 
  43. **If `Sample.ID` has more than one pair, take the first pair.**
  45.     for(i in sample.sheet %&gt;% group_by(Sample.ID) %&gt;% filter(n()&gt;2)){
  46.       # Get the pairs
  47.       pairs[[i]] &lt;- sub(&quot;\\_.*&quot;, &quot;&quot;, i)
  48.       basename &lt;- cbind(basename, pairs[[1]])
  49.     }
  51. Traceback:
  53.     Error in `[[&lt;-`(`*tmp*`, i, value = sub(&quot;\\_.*&quot;, &quot;&quot;, i)) : 
  54.       attempt to select more than one element in vectorIndex
  56. Data:
  59. Example:
  61.     &gt; dput(sample.sheet)
  62.     structure(list(File.Name = c(&quot;9d797850-f4e8-4799-8e36-f9611ce9ef99_noid_Red.idat&quot;, 
  63.     &quot;fdd60aca-ac18-43c0-b191-94fca93fb0b4_noid_Grn.idat&quot;, &quot;fdd60aca-ac18-43c0-b191-94fca93fb0b4_noid_Red.idat&quot;, 
  64.     &quot;4086487a-70af-4091-8691-a04adbdefd94_noid_Red.idat&quot;, &quot;9514c72b-27c9-4bff-bb8c-4cd809ab99cf_noid_Grn.idat&quot;, 
  65.     &quot;9514c72b-27c9-4bff-bb8c-4cd809ab99cf_noid_Red.idat&quot;, &quot;ca04f909-7afa-4feb-b160-ae0e363e2004_noid_Grn.idat&quot;, 
  66.     &quot;295b1e9d-315d-4f87-8a86-38a9c2264f00_noid_Grn.idat&quot;, &quot;6cab56c6-d37b-4bb2-b575-c0c924fe312d_noid_Grn.idat&quot;, 
  67.     &quot;71578b77-2494-4d65-8187-809a9277eb2f_noid_Grn.idat&quot;, &quot;182cce6f-eb18-4c51-9c8d-47a0770ef79d_noid_Grn.idat&quot;, 
  68.     &quot;19d2e9e5-796e-4df5-96aa-68f5d0fa1855_noid_Grn.idat&quot;, &quot;7dc90b83-0171-4600-883a-8de97c0e57cc_noid_Grn.idat&quot;, 
  69.     &quot;a3b85dd8-5621-4665-bafd-7edcf7c05aa4_noid_Red.idat&quot;, &quot;b53495eb-ca7a-455b-b45c-338ef3689ca2_noid_Grn.idat&quot;, 
  70.     &quot;69df812d-f5cc-4c1d-ac76-01530e7df677_noid_Red.idat&quot;, &quot;69df812d-f5cc-4c1d-ac76-01530e7df677_noid_Grn.idat&quot;, 
  71.     &quot;5723e331-d8e6-4687-ba89-3c0e9a8c9317_noid_Grn.idat&quot;, &quot;6445036e-69bf-4f60-a1c1-b2506e32e53c_noid_Red.idat&quot;, 
  72.     &quot;c65756c7-7ef4-4c90-ac3a-15cacf6fa83e_noid_Red.idat&quot;, &quot;4d87a92b-998b-4af6-a45b-a1cc95719597_noid_Grn.idat&quot;, 
  73.     &quot;e26a7836-17af-4498-8d69-45e86961da43_noid_Red.idat&quot;, &quot;f9233201-9029-42f1-94e1-57758062afc4_noid_Grn.idat&quot;, 
  74.     &quot;f9233201-9029-42f1-94e1-57758062afc4_noid_Red.idat&quot;, &quot;dccbe187-756d-402e-ba7f-b291f04f62c4_noid_Grn.idat&quot;, 
  75.     &quot;ca04f909-7afa-4feb-b160-ae0e363e2004_noid_Red.idat&quot;, &quot;993cba91-83c5-4383-8040-c490bd4ba0cf_noid_Red.idat&quot;, 
  76.     &quot;71578b77-2494-4d65-8187-809a9277eb2f_noid_Red.idat&quot;, &quot;913f45bd-4ac2-4411-a108-0bd1dbc16b32_noid_Grn.idat&quot;, 
  77.     &quot;913f45bd-4ac2-4411-a108-0bd1dbc16b32_noid_Red.idat&quot;, &quot;7dc90b83-0171-4600-883a-8de97c0e57cc_noid_Red.idat&quot;, 
  78.     &quot;2f29fd48-decc-40a1-8069-47dd47996474_noid_Grn.idat&quot;, &quot;d5da562f-54db-4081-b687-81dcf8b4f312_noid_Red.idat&quot;, 
  79.     &quot;13182c26-fe7f-43d3-9e0b-8d1cc980fcb8_noid_Grn.idat&quot;, &quot;9d797850-f4e8-4799-8e36-f9611ce9ef99_noid_Grn.idat&quot;, 
  80.     &quot;b53495eb-ca7a-455b-b45c-338ef3689ca2_noid_Red.idat&quot;, &quot;06f925c2-a194-4efe-98de-6a6816a64fca_noid_Red.idat&quot;, 
  81.     &quot;06f925c2-a194-4efe-98de-6a6816a64fca_noid_Grn.idat&quot;, &quot;13182c26-fe7f-43d3-9e0b-8d1cc980fcb8_noid_Red.idat&quot;, 
  82.     &quot;6cab56c6-d37b-4bb2-b575-c0c924fe312d_noid_Red.idat&quot;, &quot;6a544ba3-bb12-4995-a222-b5645505bda2_noid_Grn.idat&quot;, 
  83.     &quot;6a544ba3-bb12-4995-a222-b5645505bda2_noid_Red.idat&quot;, &quot;dccbe187-756d-402e-ba7f-b291f04f62c4_noid_Red.idat&quot;, 
  84.     &quot;59e7d51f-1d3c-4033-b8a6-3c8c77e9b535_noid_Red.idat&quot;, &quot;2c5c53d7-4812-4c05-8eb6-712ef8a48e50_noid_Grn.idat&quot;, 
  85.     &quot;af119d07-c7aa-4521-864f-d40b18f587fd_noid_Red.idat&quot;, &quot;6a0d5d91-8f46-4eb5-a600-a586dc7b9801_noid_Grn.idat&quot;, 
  86.     &quot;33c04c3b-5980-47f9-85dd-d82828553e64_noid_Red.idat&quot;, &quot;bdff5207-9d46-4b7f-ba63-cf32704363e7_noid_Grn.idat&quot;, 
  87.     &quot;30728e69-5643-4cb8-825c-0c163c3a9333_noid_Grn.idat&quot;, &quot;9217713e-0423-45af-bad1-766d1205da3a_noid_Red.idat&quot;, 
  88.     &quot;48c5eedb-542c-438e-8e92-85ea64e34776_noid_Grn.idat&quot;, &quot;48c5eedb-542c-438e-8e92-85ea64e34776_noid_Red.idat&quot;, 
  89.     &quot;e5641b0a-95af-4389-a890-4ed06cfab944_noid_Grn.idat&quot;, &quot;e5641b0a-95af-4389-a890-4ed06cfab944_noid_Red.idat&quot;, 
  90.     &quot;c1e9a16d-7244-4dbf-a8a8-36a4bf94862b_noid_Red.idat&quot;, &quot;314c0ff5-3c8e-4b01-83f9-019f6e2fcdea_noid_Red.idat&quot;, 
  91.     &quot;eeb65f09-5dc8-49b3-817a-eec283ff5bf9_noid_Grn.idat&quot;, &quot;5723e331-d8e6-4687-ba89-3c0e9a8c9317_noid_Red.idat&quot;, 
  92.     &quot;9cd0669a-ede3-4bf4-b83f-80b4990a5edc_noid_Red.idat&quot;, &quot;40510fe4-cd15-40fb-8a87-7c27e990c0a9_noid_Red.idat&quot;, 
  93.     &quot;5b856c08-b220-4d0e-8a90-0b5cdbee105e_noid_Grn.idat&quot;, &quot;2c5c53d7-4812-4c05-8eb6-712ef8a48e50_noid_Red.idat&quot;, 
  94.     &quot;ccd4e941-753b-4ebf-ac98-f3a989266c50_noid_Grn.idat&quot;, &quot;c0d8d4e6-a0cd-43f4-8b1c-c7a695603165_noid_Grn.idat&quot;, 
  95.     &quot;9217713e-0423-45af-bad1-766d1205da3a_noid_Grn.idat&quot;, &quot;4c1af618-e0e7-4c2e-b7ff-1928fe3bf77a_noid_Grn.idat&quot;, 
  96.     &quot;4c1af618-e0e7-4c2e-b7ff-1928fe3bf77a_noid_Red.idat&quot;, &quot;4fd551c8-c6ca-4068-afb9-610677a68c7b_noid_Grn.idat&quot;, 
  97.     &quot;6f03dfc0-2510-41de-808a-95b3216e1dfa_noid_Grn.idat&quot;, &quot;4086487a-70af-4091-8691-a04adbdefd94_noid_Grn.idat&quot;, 
  98.     &quot;6f03dfc0-2510-41de-808a-95b3216e1dfa_noid_Red.idat&quot;, &quot;993cba91-83c5-4383-8040-c490bd4ba0cf_noid_Grn.idat&quot;, 
  99.     &quot;7bd14ee3-3981-467c-8fe7-113b4d29fb66_noid_Red.idat&quot;, &quot;8c77b9d2-26ba-431b-aecf-7a81fa0455ee_noid_Grn.idat&quot;, 
  100.     &quot;29951bb6-c71c-462c-b620-8cae18eb0962_noid_Red.idat&quot;, &quot;0927a4a1-e872-4674-9905-6310754bcc05_noid_Red.idat&quot;, 
  101.     &quot;d3c443db-25e7-46ae-bd0c-9978390a88f8_noid_Grn.idat&quot;, &quot;c80cc68d-dde9-4cff-98c5-977098a70eaa_noid_Grn.idat&quot;, 
  102.     &quot;395c0b4f-00ac-4602-a17e-3bdb19aae54d_noid_Grn.idat&quot;, &quot;0927a4a1-e872-4674-9905-6310754bcc05_noid_Grn.idat&quot;, 
  103.     &quot;95d1a257-2641-4aa3-a732-b1f5f5732702_noid_Red.idat&quot;, &quot;43098746-2944-43cf-b3bf-bf5a92861c32_noid_Red.idat&quot;, 
  104.     &quot;f70274fc-3a63-4e6a-a5f0-be64995a119f_noid_Grn.idat&quot;, &quot;f70274fc-3a63-4e6a-a5f0-be64995a119f_noid_Red.idat&quot;, 
  105.     &quot;c1e9a16d-7244-4dbf-a8a8-36a4bf94862b_noid_Grn.idat&quot;, &quot;a1882266-9e40-4c99-b162-35a183201eaa_noid_Grn.idat&quot;, 
  106.     &quot;09eb47e3-510a-4491-99c6-d97e2e2e521c_noid_Red.idat&quot;, &quot;314c0ff5-3c8e-4b01-83f9-019f6e2fcdea_noid_Grn.idat&quot;, 
  107.     &quot;eeb65f09-5dc8-49b3-817a-eec283ff5bf9_noid_Red.idat&quot;, &quot;6445036e-69bf-4f60-a1c1-b2506e32e53c_noid_Grn.idat&quot;, 
  108.     &quot;f995f934-3a82-4c2b-93af-370714103356_noid_Grn.idat&quot;, &quot;5b856c08-b220-4d0e-8a90-0b5cdbee105e_noid_Red.idat&quot;, 
  109.     &quot;9fd697da-b3b2-408a-9b6e-c94f36824f43_noid_Grn.idat&quot;, &quot;ccd4e941-753b-4ebf-ac98-f3a989266c50_noid_Red.idat&quot;, 
  110.     &quot;29951bb6-c71c-462c-b620-8cae18eb0962_noid_Grn.idat&quot;, &quot;73f6dbe1-c74f-4337-a379-78aa0970d9e6_noid_Grn.idat&quot;, 
  111.     &quot;73f6dbe1-c74f-4337-a379-78aa0970d9e6_noid_Red.idat&quot;, &quot;40510fe4-cd15-40fb-8a87-7c27e990c0a9_noid_Grn.idat&quot;, 
  112.     &quot;0cd956b6-e061-4439-874e-9f5c09134117_noid_Red.idat&quot;, &quot;0cd956b6-e061-4439-874e-9f5c09134117_noid_Grn.idat&quot;, 
  113.     &quot;4fd551c8-c6ca-4068-afb9-610677a68c7b_noid_Red.idat&quot;, &quot;f67dbc0a-b969-48f5-86e0-d99bef15c543_noid_Grn.idat&quot;, 
  114.     &quot;1a20d2b3-5c03-4710-8aeb-2002c921a0ed_noid_Grn.idat&quot;, &quot;a3b85dd8-5621-4665-bafd-7edcf7c05aa4_noid_Grn.idat&quot;, 
  115.     &quot;b21f822a-6dfd-4146-bd22-11449585ea9d_noid_Red.idat&quot;, &quot;4313ff18-adc2-4cbc-a2d9-fe14df29a161_noid_Red.idat&quot;, 
  116.     &quot;da6348bb-d5b1-4dd5-8bd0-008c3b1a992d_noid_Grn.idat&quot;, &quot;da6348bb-d5b1-4dd5-8bd0-008c3b1a992d_noid_Red.idat&quot;, 
  117.     &quot;6b022609-0fb2-4147-9dd4-d7d49dcabe0a_noid_Red.idat&quot;, &quot;6b022609-0fb2-4147-9dd4-d7d49dcabe0a_noid_Grn.idat&quot;, 
  118.     &quot;f67dbc0a-b969-48f5-86e0-d99bef15c543_noid_Red.idat&quot;, &quot;b21f822a-6dfd-4146-bd22-11449585ea9d_noid_Grn.idat&quot;, 
  119.     &quot;06e7989a-094f-4da4-9b90-88b328f3c359_noid_Red.idat&quot;, &quot;295b1e9d-315d-4f87-8a86-38a9c2264f00_noid_Red.idat&quot;, 
  120.     &quot;1a20d2b3-5c03-4710-8aeb-2002c921a0ed_noid_Red.idat&quot;, &quot;19d2e9e5-796e-4df5-96aa-68f5d0fa1855_noid_Red.idat&quot;, 
  121.     &quot;4313ff18-adc2-4cbc-a2d9-fe14df29a161_noid_Grn.idat&quot;, &quot;2f29fd48-decc-40a1-8069-47dd47996474_noid_Red.idat&quot;, 
  122.     &quot;d5da562f-54db-4081-b687-81dcf8b4f312_noid_Grn.idat&quot;, &quot;06e7989a-094f-4da4-9b90-88b328f3c359_noid_Grn.idat&quot;, 
  123.     &quot;0f2e4e7c-8907-448f-8efb-39f80e0842e9_noid_Red.idat&quot;, &quot;0f2e4e7c-8907-448f-8efb-39f80e0842e9_noid_Grn.idat&quot;, 
  124.     &quot;9fd697da-b3b2-408a-9b6e-c94f36824f43_noid_Red.idat&quot;, &quot;af119d07-c7aa-4521-864f-d40b18f587fd_noid_Grn.idat&quot;, 
  125.     &quot;9c3d7d1c-177d-44b6-b864-d9197d0d7e96_noid_Red.idat&quot;, &quot;9c3d7d1c-177d-44b6-b864-d9197d0d7e96_noid_Grn.idat&quot;, 
  126.     &quot;d3c443db-25e7-46ae-bd0c-9978390a88f8_noid_Red.idat&quot;, &quot;c65756c7-7ef4-4c90-ac3a-15cacf6fa83e_noid_Grn.idat&quot;, 
  127.     &quot;4d87a92b-998b-4af6-a45b-a1cc95719597_noid_Red.idat&quot;, &quot;e26a7836-17af-4498-8d69-45e86961da43_noid_Grn.idat&quot;, 
  128.     &quot;23b872d1-b322-48bd-b04c-b53eecc8872c_noid_Grn.idat&quot;, &quot;23b872d1-b322-48bd-b04c-b53eecc8872c_noid_Red.idat&quot;, 
  129.     &quot;3e61019c-1c6f-4dd9-94cc-1f0ae354a761_noid_Red.idat&quot;, &quot;a1882266-9e40-4c99-b162-35a183201eaa_noid_Red.idat&quot;, 
  130.     &quot;09eb47e3-510a-4491-99c6-d97e2e2e521c_noid_Grn.idat&quot;, &quot;7bd14ee3-3981-467c-8fe7-113b4d29fb66_noid_Grn.idat&quot;, 
  131.     &quot;8c77b9d2-26ba-431b-aecf-7a81fa0455ee_noid_Red.idat&quot;, &quot;9cd0669a-ede3-4bf4-b83f-80b4990a5edc_noid_Grn.idat&quot;, 
  132.     &quot;af3b88bb-3af5-4782-8ce2-b8d0d6501c31_noid_Red.idat&quot;, &quot;af3b88bb-3af5-4782-8ce2-b8d0d6501c31_noid_Grn.idat&quot;, 
  133.     &quot;f995f934-3a82-4c2b-93af-370714103356_noid_Red.idat&quot;, &quot;3e61019c-1c6f-4dd9-94cc-1f0ae354a761_noid_Grn.idat&quot;, 
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  237.     &gt; dput(clin.info)
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  251.     &quot;TCGA.BP.5182.01&quot;, &quot;TCGA.BP.5195.01&quot;, &quot;TCGA.BP.5198.01&quot;, &quot;TCGA.BP.5199.01&quot;, 
  252.     &quot;TCGA.CJ.4869.01&quot;, &quot;TCGA.CJ.4901.01&quot;, &quot;TCGA.CJ.4912.01&quot;, &quot;TCGA.CJ.4918.01&quot;, 
  253.     &quot;TCGA.CJ.4920.01&quot;, &quot;TCGA.CJ.4923.01&quot;, &quot;TCGA.CJ.5672.01&quot;, &quot;TCGA.CJ.5675.01&quot;, 
  254.     &quot;TCGA.CJ.5676.01&quot;, &quot;TCGA.CJ.5677.01&quot;, &quot;TCGA.CJ.5682.01&quot;, &quot;TCGA.CJ.5683.01&quot;, 
  255.     &quot;TCGA.CJ.6027.01&quot;, &quot;TCGA.CJ.6030.01&quot;, &quot;TCGA.CJ.6033.01&quot;, &quot;TCGA.CW.5580.01&quot;, 
  256.     &quot;TCGA.CW.5581.01&quot;, &quot;TCGA.CW.5587.01&quot;, &quot;TCGA.CW.5590.01&quot;, &quot;TCGA.CW.6090.01&quot;, 
  257.     &quot;TCGA.CW.6093.01&quot;, &quot;TCGA.CZ.4853.01&quot;, &quot;TCGA.CZ.4856.01&quot;, &quot;TCGA.CZ.4859.01&quot;, 
  258.     &quot;TCGA.CZ.4865.01&quot;, &quot;TCGA.CZ.5451.01&quot;, &quot;TCGA.CZ.5453.01&quot;, &quot;TCGA.CZ.5456.01&quot;, 
  259.     &quot;TCGA.CZ.5459.01&quot;, &quot;TCGA.CZ.5461.01&quot;, &quot;TCGA.CZ.5462.01&quot;, &quot;TCGA.CZ.5465.01&quot;, 
  260.     &quot;TCGA.CZ.5466.01&quot;, &quot;TCGA.CZ.5468.01&quot;, &quot;TCGA.CZ.5986.01&quot;, &quot;TCGA.DV.5565.01&quot;, 
  261.     &quot;TCGA.DV.A4VX.01&quot;, &quot;TCGA.DV.A4W0.01&quot;, &quot;TCGA.EU.5905.01&quot;, &quot;TCGA.EU.5906.01&quot;, 
  262.     &quot;TCGA.G6.A5PC.01&quot;, &quot;TCGA.G6.A8L6.01&quot;, &quot;TCGA.G6.A8L7.01&quot;, &quot;TCGA.G6.A8L8.01&quot;, 
  263.     &quot;TCGA.MM.A564.01&quot;), survival = c(&quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;non-lts&quot;, 
  264.     &quot;lts&quot;, &quot;non-lts&quot;, &quot;non-lts&quot;, &quot;non-lts&quot;, &quot;non-lts&quot;, &quot;non-lts&quot;, 
  265.     &quot;non-lts&quot;, &quot;non-lts&quot;, &quot;non-lts&quot;, &quot;non-lts&quot;, &quot;non-lts&quot;, &quot;non-lts&quot;, 
  266.     &quot;non-lts&quot;, &quot;non-lts&quot;, &quot;non-lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;, 
  267.     &quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;, 
  268.     &quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;, 
  269.     &quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;non-lts&quot;, &quot;non-lts&quot;, 
  270.     &quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;non-lts&quot;, &quot;non-lts&quot;, 
  271.     &quot;non-lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;non-lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;, 
  272.     &quot;lts&quot;, &quot;non-lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;non-lts&quot;, &quot;lts&quot;, &quot;lts&quot;, 
  273.     &quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;non-lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;non-lts&quot;, 
  274.     &quot;non-lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;non-lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;non-lts&quot;, 
  275.     &quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;non-lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;, &quot;lts&quot;)), class = &quot;data.frame&quot;, row.names = c(NA, 
  276.     99L))
  279. </details>
  282. # 答案1
  283. **得分**: 0
  285. ```r
  286. library(dplyr)
  287. library(tidyr)
  289. # 使用内连接，并仅保留在两个数据集中都存在的 Sample.ID 记录
  290. inner_join(clin.info, sample.sheet, by = "Sample.ID") %>%
  291.   # 将文件名的第一部分提取为 Basename 
  292.   separate_wider_delim(File.Name, "_", names = "Basename", too_many = "drop") %>%
  293.   # 仅保留具有 2 个或更多重复项的 Basenames
  294.   filter(n() >= 2, .by = Basename) %>%
  295.   # 仅保留最多 2 个相同的 Sample.ID
  296.   slice_head(n = 2, by = Sample.ID) %>%
  297.   # 在 Basename 前添加路径
  298.   mutate(Basename = file.path(getwd(), "idat", Basename))
  299. #> # A tibble: 198 × 3
  300. #>    Sample.ID       survival Basename                                            
  301. #>    <chr>           <chr>    <chr>                                               
  302. #>  1 TCGA.A3.3357.01 lts      c:/tmp_files/idat/4d87a92b-998b-4af6-a45b-a1cc95719…
  303. #>  2 TCGA.A3.3357.01 lts      c:/tmp_files/idat/4d87a92b-998b-4af6-a45b-a1cc95719…
  304. #>  3 TCGA.A3.3367.01 lts      c:/tmp_files/idat/4fd551c8-c6ca-4068-afb9-610677a68…
  305. #>  4 TCGA.A3.3367.01 lts      c:/tmp_files/idat/4fd551c8-c6ca-4068-afb9-610677a68…
  306. #>  5 TCGA.A3.3387.01 lts      c:/tmp_files/idat/4086487a-70af-4091-8691-a04adbdef…
  307. #>  6 TCGA.A3.3387.01 lts      c:/tmp_files/idat/4086487a-70af-4091-8691-a04adbdef…
  308. #>  7 TCGA.B0.4698.01 non-lts  c:/tmp_files/idat/182cce6f-eb18-4c51-9c8d-47a0770ef…
  309. #>  8 TCGA.B0.4698.01 non-lts  c:/tmp_files/idat/182cce6f-eb18-4c51-9c8d-47a0770ef…
  310. #>  9 TCGA.B0.4710.01 lts      c:/tmp_files/idat/c1e9a16d-7244-4dbf-a8a8-36a4bf948…
  311. #> 10 TCGA.B0.4710.01 lts      c:/tmp_files/idat/c1e9a16d-7244-4dbf-a8a8-36a4bf948…
  312. #> # ℹ 188 more rows

创建于 2023-05-28，使用 reprex v2.0.2

  2. <details>
  3. <summary>英文:</summary>
  4. ``` r
  5. library(dplyr)
  6. library(tidyr)
  7. # join and keep only records with Sample.ID&#39;s that are present in both datasets
  8. inner_join(clin.info,sample.sheet, by = &quot;Sample.ID&quot;) %&gt;% 
  9. # first part of filename to Basename 
  10. separate_wider_delim(File.Name, &quot;_&quot;, names = &quot;Basename&quot;, too_many = &quot;drop&quot;) %&gt;% 
  11. # keep only Basenames with 2 or more duplicates
  12. filter(n() &gt;= 2, .by = Basename) %&gt;%
  13. # keep only up to 2 same Sample.ID&#39;s
  14. slice_head(n = 2, by = Sample.ID) %&gt;%
  15. # prepend paths to Basename
  16. mutate(Basename = file.path(getwd(),&quot;idat&quot;, Basename))
  17. #&gt; # A tibble: 198 &#215; 3
  18. #&gt;    Sample.ID       survival Basename                                            
  19. #&gt;    &lt;chr&gt;           &lt;chr&gt;    &lt;chr&gt;                                               
  20. #&gt;  1 TCGA.A3.3357.01 lts      c:/tmp_files/idat/4d87a92b-998b-4af6-a45b-a1cc95719…
  21. #&gt;  2 TCGA.A3.3357.01 lts      c:/tmp_files/idat/4d87a92b-998b-4af6-a45b-a1cc95719…
  22. #&gt;  3 TCGA.A3.3367.01 lts      c:/tmp_files/idat/4fd551c8-c6ca-4068-afb9-610677a68…
  23. #&gt;  4 TCGA.A3.3367.01 lts      c:/tmp_files/idat/4fd551c8-c6ca-4068-afb9-610677a68…
  24. #&gt;  5 TCGA.A3.3387.01 lts      c:/tmp_files/idat/4086487a-70af-4091-8691-a04adbdef…
  25. #&gt;  6 TCGA.A3.3387.01 lts      c:/tmp_files/idat/4086487a-70af-4091-8691-a04adbdef…
  26. #&gt;  7 TCGA.B0.4698.01 non-lts  c:/tmp_files/idat/182cce6f-eb18-4c51-9c8d-47a0770ef…
  27. #&gt;  8 TCGA.B0.4698.01 non-lts  c:/tmp_files/idat/182cce6f-eb18-4c51-9c8d-47a0770ef…
  28. #&gt;  9 TCGA.B0.4710.01 lts      c:/tmp_files/idat/c1e9a16d-7244-4dbf-a8a8-36a4bf948…
  29. #&gt; 10 TCGA.B0.4710.01 lts      c:/tmp_files/idat/c1e9a16d-7244-4dbf-a8a8-36a4bf948…
  30. #&gt; # ℹ 188 more rows

<sup>Created on 2023-05-28 with reprex v2.0.2</sup>

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  • 本文由 发表于 2023年5月28日 05:31:38
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