Why won't this list of strings store as a variable in R?

Question

[emilyc]

Hello/bonjour,

I really cannot figure out the reason I am getting an error with the below when executed in R.

RNA1 <- c("ARE85692.1", "WP_030538461.1", "OLA28585.1", "WP_030092979.1", "WP_011255103.1", "WP_037470143.1", "WP_037470142.1","WP_048575187.1", "WP_040265129.1", "WP_112366619.1", "OZS41314.1", "AGH47784.1", "KSV62316.1", "WP_052448286.1", "WP_063735071.1", "KYL83848.1", "WP_012644006.1", "WP_051849361.1", "ACF68028.1", "OJY67256.1", "EHV83032.1", "XP_020442226.1", "RGU03766.1", "WP_000904906.1", "PTR09915.1", "EKU54097.1", "WP_104504265.1", "AEA08378.1", "WP_084929469.1", "AKN19375.1", "CLP57205.1", "WP_071925129.1", "WP_066491086.1", "PZU06012.1", "WP_030199248.1", "XP_025029738.1", "RCN39061.1", "WP_026925198.1", "XP_013869014.1", "WP_085810747.1", "CRY96001.1", "ONH68315.1", "ASG92531.1", "XP_021849475.1", "XP_006401694.1", "WP_096234110.1", "WP_086730043.1", "WP_072340239.1", "WP_031455762.1", "WP_011565327.1", "XP_026410054.1", "OEU57032.1", "WP_063357489.1", "YP_009329821.1", "WP_054311735.1", "WP_069548609.1", "GBG31406.1", "WP_077692070.1", "PFH62043.1", "WP_093049484.1", "XP_022039943.1", "PRP78866.1", "XP_018737851.1", "RMY65069.1", "RKY44823.1", "YP_009329976.1", "YP_009333557.1", "WP_119236352.1", "ODT01658.1", "XP_021940059.1", "WP_090634955.1", "XP_020190111.1", "PVU98352.1", "YP_009337427.1", "ASM94072.1", "WP_106566124.1", "ASM94072.1", "WP_005183695.1", "EOA18517.1", "WP_031514849.1", "WP_121631597.1", "WP_029313977.1", "WP_031514849.1", "WP_121631597.1", "WP_029313977.1", "YP_009333388.1", "WP_039951580.1", "YP_009333424.1", "WP_076143666.1", "KIR87973.1", "WP_111579388.1", "XP_011395463.1", "WP_094786685.1", "AGZ83338.1", "OIP93066.1", "XP_014283183.1", "WP_009740728.1", "PYO78928.1", "PYM36611.1", "AOZ73397.1", "KYK23134.1", "WP_073281990.1", "WP_115122543.1", "WP_003648784.1", "YP_009237556.1", "YP_009333186.1", "YP_009333507.1", "XP_013368103.1", "XP_018782030.1", "WP_114764940.1", "WP_082342709.1", "XP_026614825.1", "WP_096746960.1", "WP_093320012.1", "ARU76991.1", "AFR11835.1", "XP_002910093.1", "WP_073176644.1", "WP_086490062.1", "RHN80591.1", "WP_062831894.1", "CDB02563.1", "GAX95753.1", "AXQ65872.1", "XP_023329285.1", "WP_004082834.1", "WP_013307564.1", "KFV82731.1", "WP_031138773.1", "XP_020682540.1", "APG76144.1", "WP_035114579.1", "WP_006284965.1", "WP_096474323.1", "WP_042681208.1", "WP_097150106.1", "AAW51878.1", "SET36711.1", "KFP07431.1", "WP_071357402.1", "PZO55424.1", "WP_018341803.1", "WP_018341803.1", "XP_020578684.1", "XP_016347362.1", "CZR67299.1", "KFX48225.1", "CZR67299.1", "SOE19862.1", "YP_009337755.1", "AWK77840.1", "KKW02112.1", "APG76452.1", "ASM94018.1", "YP_009333600.1", "YP_009333601.1", "PYU14395.1", "WP_069185297.1", "YP_009337082.1", "YP_009330048.1", "AUM61889.1", "XP_012339246.1", "WP_010100069.1", "YP_009333384.1", "OEG70557.1", "CEL73936.1", "WP_072887783.1", "XP_020574395.1", "YP_009342290.1", "AFF57920.1", "YP_009330042.1", "ORY25512.1", "OJU61881.1", "ETL37738.1", "EKD65879.1", "XP_008889488.1", "WP_103061524.1", "YP_009330042.1", "WP_105635083.1", "XP_020691136.1", "EPB92962.1", "WP_035470959.1", "KIK35098.1", "WP_053655326.1", "KRT66746.1", "RIK26981.1", "CDL24210.1", "GAB94973.1", "YP_001039741.1", "OCT97283.1", "NP_193640.4", "XP_007365969.1", "PYN94992.1", "WP_115971353.1", "WP_030195772.1", "WP_090992472.1", "XP_018762443.1", "YP_009330008.1", "AVH80932.1", "WP_112380387.1", "PRY26922.1", "CQD23474.1", "WP_010408743.1", "WP_106130445.1", "EAQ33519.1", "KXW55186.1", "KXI15614.1", "XP_024359367.1", "OGE31818.1", "YP_009337883.1", "AGT15715.1", "XP_014737065.1", "AGZ83336.2", "AFM44928.2", "WP_004727033.1", "CDA25608.1", "WP_100205692.1", "WP_028109468.1", "YP_009337671.1", "XP_024875031.1", "XP_014145525.1", "XP_020474819.1", "XP_005061300.1", "SIO87404.1", "CEI98194.1", "WP_019528182.1", "XP_014530733.1", "OLZ29151.1", "XP_016180396.1", "KFB98075.1", "WP_051506973.1", "XP_020780343.1", "RJU90914.1", "WP_048426347.1", "SIR30680.1", "XP_005051765.1", "APG76171.1", "APG76598.1", "EMP55287.1", "YP_009336792.1", "XP_007001859.1", "KXS96290.1", "OON05112.1", "YP_009109631.1", "OMJ77737.1", "AJD07497.1", "PYL28269.1", "XP_021863274.1", "WP_004160142.1", "OTA70178.1", "YP_398835.1", "RIW43611.1", "XP_022910622.1", "WP_107712039.1", "OMO51929.1", "WP_071550802.1", "WP_088469378.1", "SUX89036.1", "CBA31922.1", "CZR19882.1", "KTC66800.1", "WP_085515616.1", "YP_009333600.1", "YP_654545.1", "YP_654545.1", "OHB51241.1", "PIO64269.1", "EDK39810.2", "XP_013363451.1", "PHS21967.1", "WP_083520182.1", "OAQ67482.1", "WP_104331052.1", "CAX33877.1", "STX28550.1", "YP_009449401.1", "YP_009333557.1", "WP_114380100.1", "KKS15734.1", "PKY48696.1", "OWK58877.1", "WP_119795562.1", "GAX86195.1", "AAB94620.1", "WP_009694801.1", "AWK77840.1", "PCF46882.1", "WP_009060397.1", "AJP36355.1", "YP_009336791.1", "WP_075151084.1", "WP_100304320.1", "YP_009333437.1", "YP_009337854.1", "XP_025388358.1", "WP_103312029.1", "XP_009517785.1", "YP_009337045.1", "WP_115390984.1", "WP_083885471.1", "PZP85870.1", "APQ44496.1", "WP_025425191.1", "AAX26869.1", "PHT27344.1", "WP_017430083.1", "WP_088642165.1", "CDJ81252.1", "XP_007130401.1", "WP_090235612.1", "WP_021278083.1", "OGJ57224.1", "OFW09128.1", "WP_104635294.1", "ASM94017.1", "ETL31718.1", "WP_071814864.1", "WP_043211725.1", "EPS42677.1", "YP_009337772.1", "YP_009330042.1", "YP_009329862.1", "RMZ28204.1", "AAD24412.1", "WP_062451953.1", "OXE37212.1", "WP_090474888.1", "WP_114909516.1", "WP_093034338.1", "WP_041782265.1", "WP_046232340.1", "YP_009336927.1", "WP_008191349.1", "SLE30469.1", "EFL15839.1", "EID19494.1", "EFE84358.1", "SPF69569.1", "WP_120491108.1", "WP_087006979.1", "WP_039875332.1", "APG76184.1", "SUX89036.1", "CBA31922.1", "KOT11881.1", "ADI16723.1", "AOE05674.1", "AOE10198.1", "AOE10199.1", "AQK66169.1", "KJS33120.1", "WP_013995201.1", "WP_089591822.1", "ASM94093.1", "KMS64820.1", "AOE07163.1", "AOE07164.1", "AOE11734.1", "AOE07606.1", "APQ44493.1", "APQ44496.1", "YP_009333600.1", "AOE10200.1", "SPY22707.1", "XP_021891377.1", "BAK20600.1", "XP_018733639.1", "XP_005383010.1", "OGX05865.1", "AFM44928.2", "YP_009337445.1", "AHA86934.1", "WP_036204856.1", "WP_055080489.1", "XP_018734836.1", "YP_009336700.1", "WP_115823841.1", "XP_025262873.1", "XP_006916488.1", "WP_084329043.1", "WP_015347430.1", "XP_814918.1", "WP_015284209.1", "KOB71805.1", "RBP18207.1", "ASM94017.1", "WP_056655483.1", "YP_007438853.1", "XP_024908946.1", "WP_117872353.1", "AKH67441.1", "PZX36280.1", "ORY42375.1", "CEO96512.1", "XP_002671596.1", "OJI06181.1", "YP_009337230.1", "AYN75542.1", "WP_031470382.1", "WP_051737908.1", "WP_112948296.1", "YP_009337111.1", "RLJ02486.1", "YP_009342270.1", "KUK29015.1", "CQD23510.1", "WP_090423511.1", "KQS54592.1", "SWW83940.1", "WP_061772349.1", "XP_013650435.1", "KIK72446.1", "WP_035344944.1", "WP_019617976.1", "YP_009337445.1", "WP_083642681.1", "YP_009337419.1", "WP_112094499.1", "OCB87632.1", "YP_009329821.1", "EEP55936.1", "WP_075172010.1", "WP_089221271.1", "WP_092405127.1", "WP_087307961.1", "OUS08811.1", "XP_021707674.1", "WP_073193414.1", "APG76212.1", "WP_060167633.1", "KZC89585.1", "WP_112148229.1", "WP_100645044.1", "WP_112380386.1", "WP_030092974.1", "RMG50508.1", "OFY65797.1", "WP_074310443.1", "RLV95769.1", "YP_009336636.1", "APG77045.1", "WP_082633868.1", "APG77046.1", "KTC66578.1", "KHG25866.1", "XP_022538281.1", "WP_102365619.1", "KGJ03428.1", "WP_047867244.1", "GAM02817.1", "WP_047867245.1", "WP_049570233.1", "PYI30954.1", "WP_099543287.1", "WP_106457008.1", "ASM94018.1", "WP_020590223.1", "YP_009336792.1", "YP_392465.1", "WP_076067437.1", "XP_024386541.1", "OLS15339.1", "XP_016526832.1", "CEM06887.1", "WP_107660914.1", "WP_118990021.1", "WP_048381386.1", "WP_030939398.1", "APG77253.1", "XP_022031898.1", "SAM01137.1", "WP_075585659.1", "WP_075153469.1", "GBH14995.1", "WP_007407197.1", "AWN14257.1", "WP_097297685.1", "AOX46253.1", "KHS45135.1", "XP_006776713.1", "WP_088296610.1", "YP_009333150.1", "RKY44687.1", "XP_008875055.1", "YP_009333545.1", "YP_392465.1", "WP_074834324.1", "XP_009063951.1", "PKS10204.1", "WP_108850444.1", "WP_062386622.1", "PHT30680.1", "AAO24320.1", "WP_045185214.1", "YP_009329821.1", "KXQ43755.1", "OQY64528.1", "ADI17229.1", "CAJ30045.1", "SMG06634.1", "WP_061773072.1", "WP_107953972.1", "KDO81281.1", "CAX33878.1", "WP_015329842.1", "XP_005775359.1", "OYV07171.1", "WP_088086110.1", "XP_007017423.2", "YP_009337704.1", "CDQ86554.1", "WP_091009173.1", "XP_023952606.1", "WP_055438060.1", "OJW01441.1", "XP_014609874.1", "AXY86077.1", "WP_087974390.1", "CEJ90739.1", "KYN31989.1", "YP_009330023.1", "AXQ51448.1", "WP_066630827.1", "RMX74157.1", "WP_092247952.1", "WP_116678544.1", "XP_020487964.1", "WP_062230413.1", "WP_056617232.1", "XP_021910847.1", "XP_017768995.1", "OAF16132.1", "WP_107525136.1", "WP_119493636.1", "WP_082748398.1", "WP_042490936.1", "CEE80498.1", "RGS16953.1", "AYE66860.1", "CDQ90625.1", "EDM70192.1", "XP_011697304.1", "KFD96747.1", "XP_001746844.1", "WP_086732958.1", "AAR32107.1", "WP_024524936.1", "WP_121848546.1", "WP_096684028.1", "APG76841.1", "CAJ30046.1", "WP_019005849.1", "PPR79129.1", "WP_121471861.1", "YP_009333601.1", "WP_018191362.1", "GAE78858.1", "WP_075260779.1", "RAV32216.1", "PZQ69074.1", "AGZ83336.2", "BAG46935.1", "OCL12566.1", "WP_083417402.1", "OON04083.1", "WP_103123647.1", "WP_052178944.1", "WP_079125492.1", "PSR90737.1", "RMG95085.1", "XP_011571352.1", "RMJ27228.1", "OLP82095.1", "WP_008618938.1", "SFB48779.1", "XP_010085865.1", "KIK45414.1", "WP_068433130.1", "KDB14550.1", "AAA87625.1", "GAT56413.1", "XP_004338718.1", "KIL88497.1", "YP_001429583.1", "WP_073397577.1", "AOY34458.1", "YP_009329863.1", "ANA08048.1", "KRO88946.1", "WP_007078151.1", "XP_010155229.1", "EMS52259.1", "XP_020434888.1", "WP_121368830.1", "CDB39267.1", "PXY51748.1", "PIE80481.1", "CEP18960.1", "XP_012227353.1", "RGP63998.1", "WP_107099300.1", "XP_024139964.1", "RMX47585.1", "XP_007373726.1", "EAQ35133.1", "WP_010339210.1", "SOC89939.1", "KIY12868.1", "WP_058600399.1", "WP_082052479.1", "CNJ48920.1", "YP_009337800.1", "XP_002619317.1", "AHJ61123.1", "EEW79284.1", "CCG06601.1", "CCG06582.1", "YP_009333352.1", "WP_029449191.1", "PCJ51959.1", "OAJ11263.1", "KLC40008.1", "WP_083966399.1", "WP_052597349.1", "CDW72166.1", "EJY85214.1", "WP_007405213.1", "XP_014062671.1", "GAM01020.1", "CDQ29749.1", "YP_009362296.1", "XP_017240548.1", "OFQ97201.1", "XP_018267507.1", "XP_007700505.1", "XP_023904983.1", "PHT26618.1", "ASM94018.1", "EFG00476.1", "KRY33441.1", "CDQ90285.1", "WP_028535927.1", "WP_086607027.1", "PAV92842.1", "WP_014241917.1", "WP_113667938.1", "XP_018330205.1", "GAU96577.1", "AKQ01593.1", "WP_011563027.1", "CKY60557.1", "WP_006099521.1", "EJY76437.1", "WP_111375676.1", "WP_026532066.1", "WP_082420995.1")

Error: unexpected symbol in:
"#store accession numbers
RNA1 <- c("ARE85692.1"

Sorry it is long. This was composed using unix commands and is not manually composed. Does R have a limit for the number of strings that can be stored?

The example below stores fine:

RNAtest <- c("ARE85692.1", "WP_030538461.1")
 print(RNAtest)
[1] "ARE85692.1"     "WP_030538461.1"

Thank you in advance, sorry for the simple issue. My thoughts are that it's beyond a grammatical error, but I could be very wrong.

[ATpoint]

Probably missing quotations somewhere. It is bad practice to read long objects like this into R directly for exactly the reason you see. The object is so long that you cannot visually inspect it for correct quoting and formatting. Don't you have these as a file and can import them via reading the entire file?

[emilyc]

Yes, it's a separate file completely manipulated in unix, none of it is manual. I've copied and pasted it into R just because I am sending this complete script to someone who doesn't understand how to use R. It's exactly the same in the file that I read in.

[Kevin Blighe]

Try outside RStudio, if at all possible.

It works fine for me (here, I shortened it).; however, I believe that my R version detects the maximum limit and creates a newline itself:

RNA1 <- c("ARE85692.1", "WP_030538461.1", "OLA28585.1", "WP_030092979.1", "WP_011255103.1", "WP_037470143.1", "WP_037470142.1","WP_048575187.1", "WP_040265129.1", "WP_112366619.1", "OZS41314.1", "AGH47784.1", "KSV62316.1", "WP_052448286.1", "WP_063735071.1", "KYL83848.1", "WP_012644006.1", "WP_051849361.1", "ACF68028.1", "OJY67256.1", "EHV83032.1", "XP_020442226.1", "RGU03766.1", ... "OFQ97201.1", "XP_018267507.1", "XP_007700505.1", "XP_023904983.1", "PHT26618.1", "ASM94018.1", "EFG00476.1", "KRY33441.1", "CDQ90285.1", "WP_028535927.1", "WP_086607027.1", "PAV92842.1", "WP_014241917.1", "WP_113667938.1", "XP_018330205.1", "GAU96577.1", "AKQ01593.1", "WP_011563027.1", "CKY60557.1", "WP_006099521.1", "EJY76437.1", "WP_111375676.1", "WP_026532066.1", "WP_082420995.1")

length(RNA1)
[1] 656


sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                            LC_TIME=English_United Kingdom.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_3.6.0

[emilyc]

yes, I tried in the terminal directly. The same issue occurs. I can shorten it and get it to work also, but I was hoping to avoid having to do this. Thanks for the help!

Answer 1

[Benn]

There is a maximum of what fits in one line in the R console. So use new lines, for example only 5-10 accessions on one line (also for your own legibility).

[emilyc]

Do you have any idea of the actual limit? Based on this I can manipulate it outside of R. Thanks either way.

[Benn]

I think 4096 characters, but I am not sure.

[emilyc]

Ah it's by characters - that makes more sense. Awesome, thank you!

[Asaf]

Hi @emilyc, if you think this is the answer you should accept it for recognition and future reference. Thanks