如何在stringdist中使用grabl function为多个output向量创建循环

Question

I'm trying to create a loop for the grabl function in stringdist that repeats the followings steps:

• pick a string pattern from a vector and insert as p_i
• match with strings in table x
• create output vector vec_i
• repeat for all i = 1, ..., n

so that, in the end, I yield n output vectors

grabl(x, pattern, maxDist = )

#my x is a column of a data frame with variable number of rows
> print(year2002$References[1:3])
[1] "Angelini, S., Moreno, R., Gouffi, K., Santini, C.-L., Yamagishi, A., Berenguer, J., Wu, L.-F., Export of Thermus thermophilus alkaline phosphatase via the twin-arginine translocation pathway in Escherichia coli (2001) FEBS Lett., 506, pp. 103-107; Bernhard, M., Friedrich, B., Siddiqui, R.A., Ralstonia eutropha TF93 is blocked in tat-mediated protein export (2000) J. Bacteriol., 182, pp. 581-588; Blaudeck, N., Sprenger, G.A., Freudl, R., Wiegert, T., Specificity of signal peptide recognition in tat-dependent bacterial protein translocation (2001) J. Bacteriol., 183, pp. 604-610; Bogsch, E., Sargent, F., Stanley, N.R., Berks, B.C., Robinson, C., Palmer, T., An essential component of a novel bacterial protein export system with homologues in plastids and mitochondria (1998) J. Biol. Chem., 273, pp. 18003-18006; Chanal, A., Santini, C.-L., Wu, L.-F., Potential receptor function of three homologous components, TatA, TatB and TatE, of the twin-arginine signal sequence-dependent metalloenzyme translocation pathway in Escherichia coli (1998) Mol. Microbiol., 30, pp. 674-676; Cristobal, S., De Gier, J.-W., Nielsen, H., Von Heijne, G., Competition between Sec- and TAT-dependent protein translocation in Escherichia coli (1999) EMBO J., 18, pp. 2982-2990; Dion, M., Fourage, L., Hallet, J.N., Colas, B., Cloning and expression of a beta-glycosidase gene from Thermus thermophilus. Sequence and biochemical characterization of the encoded enzyme (1999) Glycoconj. J., 16, pp. 27-37; Guzman, L.-M., Belin, D., Carson, M.J., Beckwith, J., Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter (1995) J. Bacteriol., 177, pp. 4121-4130; Halbig, D., Wiegert, T., Blaudeck, N., Freudl, R., Sprenger, G.A., The efficient export of NADP-containing glucose-fructose oxidoreductase to the periplasm of Zymomonas mobilis depends both on an intact twin-arginine motif in the signal peptide and on the generation of a structural export signal induced by cofactor binding (1999) Eur. J. Biochem., 263, pp. 543-551; Heikkila, M.P., Honisch, U., Wunsch, P., Zumft, W.G., Role of the Tat transport system in nitrous oxide reductase translocation and cytochrome cd1 biosynthesis in Pseudomonas stutzeri (2001) J. Bacteriol., 183, pp. 1663-1671; Ito, K., Akiyama, Y., Yura, T., Shiba, K., Diverse effects of the MalE-LacZ hybrid protein on Escherichia coli cell physiology (1986) J. Bacteriol., 167, pp. 201-204; Jongbloed, J.D., Martin, U., Antelmann, H., Hecker, M., Tjalsma, H., Venema, G., Bron, S., Muller, J., TatC is a specificity determinant for protein secretion via the twin- arginine translocation pathway (2000) J. Biol. Chem., 275, pp. 41350-41357; Kiino, D.R., Phillips, G.J., Silhavy, T.J., Increased expression of the bifunctional protein PrlF suppresses overproduction lethality associated with exported beta-galactosidase hybrid proteins in Escherichia coli (1990) J. Bacteriol., 172, pp. 185-192; Manoil, C., Analysis of protein localization by use of gene fusions with complementary properties (1990) J. Bacteriol., 172, pp. 1035-1042; Manoil, C., Bailey, J., A simple screen for permissive sites in proteins: Analysis of Escherichia coli lac permease (1997) J. Mol. 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Microbiol., 41, pp. 241-246; Santini, C.-L., Bernadac, A., Zhang, M., Chanal, A., Ize, B., Blanco, C., Wu, L.-F., Translocation of jellyfish green fluorescent protein via the Tat system of Escherichia coli and change of its periplasmic localization in response to osmotic up-shock (2001) J. Biol. Chem., 276, pp. 8159-8164; Santini, C.L., Ize, B., Chanal, A., Müller, M., Giordano, G., Wu, L.-F., A novel Sec-independent periplasmic protein translocation pathway in Escherichia coli (1998) EMBO J., 17, pp. 101-112; Sargent, F., Bogsch, E.G., Stanley, N.R., Wexler, M., Robinson, C., Berks, B.C., Palmer, T., Overlapping functions of components of a bacterial Sec-independent protein export pathway (1998) EMBO J., 17, pp. 3640-3650; Sargent, F., Stanley, N.R., Berks, B.C., Palmer, T., Sec-independent protein translocation in Escherichia coli: A distinct and pivotal role for the TatB protein (1999) J. Biol. Chem., 274, pp. 36073-36082; Schaerlaekens, K., Schierova, M., Lammertyn, E., Geukens, N., Anne, J., Van Mellaert, L., Twin-arginine translocation pathway in Streptomyces lividans (2001) J. Bacteriol., 183, pp. 6727-6732; Schatz, G., Dobberstein, B., Common principles of protein translocation across membranes (1996) Science, 271, pp. 1519-1526; Settles, A.M., Yonetani, A., Baron, A., Bush, D.R., Cline, K., Martienssen, R., Sec-independent protein translocation by the maize Hcf106 protein (1997) Science, 278, pp. 1467-1470; Snyder, W.B., Silhavy, T.J., Beta-galactosidase is inactivated by intermolecular disulfide bonds and is toxic when secreted to the periplasm of Escherichia coli (1995) J. Bacteriol., 177, pp. 953-963; Stanley, N.R., Findlay, K., Berks, B.C., Palmer, T., Escherichia coli strains blocked in Tat-dependent protein export exhibit pleiotropic defects in the cell envelope (2001) J. Bacteriol., 183, pp. 139-144; Stanley, N.R., Palmer, T., Berks, B.C., The twin arginine consensus motif of Tat signal peptides is involved in Sec-independent protein targeting in Escherichia coli (2000) J. Biol. Chem., 275, pp. 11591-11596; Stanley, N.R., Sargent, F., Buchanan, G., Shi, J., Stewart, V., Palmer, T., Berks, B.C., Behaviour of topological marker proteins targeted to the Tat protein transport pathway (2002) Mol. Microbiol., 43, pp. 1005-10021; Tamakoshi, M., Uchida, M., Tanabe, K., Fukuyama, S., Yamagishi, A., Oshima, T., A new Thermus-Escherichia coli shuttle integration vector system (1997) J. Bacteriol., 179, pp. 4811-4814; Tommassen, J., Leunissen, J., Van Damme-Jongsten, M., Overduin, P., Failure of E. coli K-12 to transport PhoE-LacZ hybrid proteins out of the cytoplasm (1985) EMBO J., 4, pp. 1041-1047; Vieille, C., Zeikus, G.J., Hyperthermophilic enzymes: Sources, uses, and molecular mechanisms for thermostability (2001) Microbiol. Mol. Biol. Rev., 65, pp. 1-43; Voulhoux, R., Ball, G., Ize, B., Vasil, M.L., Lazdunski, A., Wu, L.F., Filloux, A., Involvement of the twin-arginine translocation system in protein secretion via the type II pathway (2001) EMBO J., 20, pp. 6735-6741; Weiner, J.H., Bilous, P.T., Shaw, G.M., Lubitz, S.P., Frost, L., Thomas, G.H., Cole, J., Turner, R.J., A novel and ubiquitous system for membrane targeting and secretion of cofactor-containing proteins (1998) Cell, 93, pp. 93-101; Wexler, M., Sargent, F., Jack, R.L., Stanley, N.R., Bogsch, E.G., Robinson, C., Berks, B.C., Palmer, T., TatD is a cytoplasmic protein with DNase activity. No requirement for TatD family proteins in sec-independent protein export (2000) J. Biol. Chem., 275, pp. 16717-16722; Wu, L.-F., Ize, B., Chanal, A., Quentin, Y., Fichant, G., Bacterial twin-arginine signal peptide-dependent protein translocation pathway: Evolution and mechanism (2000) J. Mol. Microbiol. Biotechnol., 2, pp. 179-189; Yahr, T.L., Wickner, W.T., Functional reconstitution of bacterial Tat translocation in vitro (2001) EMBO J., 20, pp. 2472-2479"
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Cycling Agroecosyst., 58, pp. 367-375; Aulakh, M.S., Wassmann, R., Rennenberg, H., Fink, S., Pattern and amount of aerenchyma relate to variable methane transport capacity of different rice cultivars (2000) Plant Biol., 2, pp. 182-194; Aulakh, M.S., Wassmann, R., Bueno, C., Kreuzwieser, J., Rennenberg, H., Characterization of root exudates at different growth stages of ten rice (Oryza sativa L.) cultivars (2001) Plant Biol., 3, pp. 139-148; Aulakh, M.S., Wassmann, R., Bueno, C., Rennenberg, H., Impact of root exudates of different cultivars and plant developmental stages of rice (Oryza sativa L.) on methane production in a paddy soil (2001) Plant Soil, 230, pp. 77-86; Aulakh, M.S., Wassmann, R., Rennenberg, H., Methane emissions from rice fields - Quantification, role of management, and mitigation options (2001) Adv. Agron., 70, pp. 193-260; Bartolome, V.I., Casumpang, R.M., Ynalvez, M.A.H., Olea, A.B., McLaren, C.G., (1999) IRRISTAT for Windows - Statistical software for agricultural research, , Biometrics, International Rice Research Institute, Los Banos, the Philippines; Butterbach-Bahl, K., Papen, H., Rennenberg, H., Impact of gas transport through rice cultivars on methane emission from rice paddy fields (1997) Plant Cell Environ., 20, pp. 1175-1183; Cochran, W.G., Cox, G.M., (1950) Experimental Designs, , Wiley, New York; Gomez, K.A., (1972) Techniques for field experiments with rice, , International Rice Research Institute, Los Banos, the Philippines; Kesheng, S., Zhen, L., Effect of rice cultivars and fertilizer management on methane emission in a rice paddy in Beijing (1997) Nutr. Cycling Agroecosyst., 49, pp. 139-146; Lu, Y., Wassmann, R., Neue, H.U., Bueno, C.S., Huang, C., Response of methanogenesis in anaerobic rice soils to exogenous substrates (2000) Soil Biol. Biochem., 32, pp. 1683-1690; Minami, K., Neue, H.U., Rice paddies as a methane source (1994) Climate Change, 27, pp. 13-26; Minoda, T., Kimura, M., Contribution of photosynthesized carbon to the methane emitted from paddy fields (1994) Geophys. Res. Lett., 21, pp. 2007-2010; Mitra, S., Jain, M.C., Kumar, S., Bandyopadhya, S.K., Kalra, N., Effect of rice cultivars on methane emission (1999) Agri. Ecosyst. Environ., 73, pp. 177-183; Rennenberg, H., Wassmann, R., Papen, H., Seiler, W., Trace gas emission in rice cultivation (1992) Ecol. Bull., 42, pp. 164-173; Sass, R.L., Fisher, F.M., Harcombe, P.A., Turner, F.T., Mitigation of methane emission from rice fields: Effect of incorporated rice straw (1991) Global Biogeochem. Cycles, 5, pp. 275-288; Shalini, S., Kumar, S., Jain, M.C., Methane emission from two Indian soils planted with different rice cultivars (1997) Biol. Fertil. Soils, 25, pp. 285-289; Sigren, L.K., Byrd, G.T., Fisher, F.M., Sass, R.L., Comparison of soil acetate concentrations and methane production, transport, and emission in two rice cultivars (1997) Global Biochem. Cycles, 11, pp. 1-14; Wang, B., Neue, H.U., Samonte, H.P., Effect of cultivar difference (IR72, IR65598 and Dular) on methane emission (1997) Agri. Ecosyst. Environ., 62, pp. 31-40; Wassmann, R., Aulakh, M.S., The role of rice plants in regulating mechanisms of methane emissions (2000) Biol. Fertil. Soils, 31, pp. 20-29; Wassmann, R., Lantin, R.S., Neue, H.U., Buendia, L.V., Corton, T.M., Lu, Y., Characterization of methane emissions in Asia. Part 3. Mitigation options and future research needs (2000) Nutr. Cycling Agroecosyst., 58, pp. 23-36; Watanabe, A., Kajiwara, M., Tashiro, T., Kimura, M., Influence of rice cultivar on methane emission from paddy fields (1995) Plant Soil, 17, pp. 51-56"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
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Helsinki, Finland; Chalon, A., Bastin, G., Installe, M., Identification of a biomethanization process: A case study (1982) IFAC Symp on identification and system parameter estimation, pp. 409-413. , Washington DC USA; Chappell, M.J., Godfrey, K.R., Vajda, S., Global identifiability of the parameters of nonlinear systems with special inputs: A comparison of methods (1990) Math Biosci, 102, pp. 41-73; Cox, D.R., Hinkley, C.V., (1974) Theoretical statistics, , Bekeg GA, Soredis GU, editors. Chapman & Hall; Denis-Vidal, L., Joly-Blanchard, Gh., Noiret, C., (2001) Some effective approaches to check the identifiability of uncontrolled nonlinear systems, 57, pp. 35-44; Dochain, D., Vanrolleghem, P.A., Van Daele, M., Structural identifiability of biokinetic models of activated sludge respiration (1995) Wat Res, 11, pp. 2571-2578; Forster, C., Wase, D., (1990) Environmental biotechnology, , Chichester. 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#my patterns p_i come from a different data frame also with variable number of rows
print(ref_year2002$Title[1:10])
 [1] "Struc3ture and mechanism of chalcone synthase-like polyketide synthases"                                                                                                  
 [2] "Role of Acinetobacter for biodegradability of quaternary ammonium compounds"                                                                                              
 [3] "Modeling of carbonaceous particles emitted by boreal and temperate wildfires at northern latitudes"                                                                       
 [4] "Estimation of the microcystin content in cyanobacterial field samples from German lakes using the colorimetric protein-phosphatase inhibition assay and RP-HPLC"          
 [5] "Microcystins (hepatotoxic heptapeptides) in German fresh water bodies"                                                                                                    
 [6] "Immunogenic efficacy of differently produced recombinant vaccines candidates against Pseudomonas aeruginosa infections"                                                   
 [7] "Mapping the biomass of Bornean tropical rain forest from remotely sensed data"                                                                                            
 [8] "Altered physiological and growth responses to elevated [CO2] in offspring from holm oak (Quercus ilex L.) mother trees with lifetime exposure to naturally elevated [CO2]"
 [9] "Substrate specificities of the chloromuconate cycloisomerases from Pseudomonas sp. B13, Ralstonia eutropha JMP134 and Pseudomonas sp. P51"                                
[10] "Surface reconstitution of a de novo synthesized hemoprotein for bioelectronic applications"

for now my approach is to use the for loop, but I'm not very good at this

for (i in ref_year2002$Title[1:126])
    c(grabl(year2002$References, i, maxDist = 8))

So far the code, unsurprisingly, does not yield any results.

• Can I pull the values directly from the data frame or do I have to create a vector in the code and how do I do this?
• How can I create an output vector for each iteration?

I'm grateful for any helpful idea!

Jonas

Answer 1

Something like the following might do what you want. Untested, since there is no data.

# create a list to hold the results beforehand
results_list <- vector("list", length = 126)
for(i in 1:126) {
  results_list[[i]] <- grabl(year2002$References, ref_year2002$Title[i], maxDist = 8))
}