I fail to export a dataframe produced by uco(seqinr) function in rscu computation. What means should I use?. The dataframe is not showing in r environment either, it only remain in the console. Have tried so much copying it to excel, word, notepad in vain. Could someone help?
> library("seqinr")
> rcds <- read.fasta("virus.fasta")[[1]]
> uco( rcds, index = "freq")
aaa aac aag aat aca acc
0.068669528 0.025751073 0.004291845 0.030042918 0.030042918 0.012875536
acg act aga agc agg agt
0.008583691 0.012875536 0.034334764 0.000000000 0.008583691 0.025751073
ata atc atg att caa cac
0.025751073 0.012875536 0.017167382 0.034334764 0.017167382 0.008583691
cag cat cca ccc ccg cct
0.008583691 0.004291845 0.017167382 0.004291845 0.004291845 0.008583691
cga cgc cgg cgt cta ctc
0.008583691 0.000000000 0.000000000 0.004291845 0.004291845 0.012875536
ctg ctt gaa gac gag gat
0.012875536 0.008583691 0.008583691 0.004291845 0.021459227 0.012875536
gca gcc gcg gct gga ggc
0.021459227 0.004291845 0.000000000 0.008583691 0.017167382 0.000000000
ggg ggt gta gtc gtg gtt
0.004291845 0.012875536 0.008583691 0.000000000 0.008583691 0.012875536
taa tac tag tat tca tcc
0.047210300 0.017167382 0.034334764 0.047210300 0.008583691 0.017167382
tcg tct tga tgc tgg tgt
0.004291845 0.004291845 0.034334764 0.017167382 0.025751073 0.012875536
tta ttc ttg ttt
0.017167382 0.017167382 0.034334764 0.038626609
> uco( rcds, index = "eff")
aaa aac aag aat aca acc acg act aga agc agg agt ata atc atg att caa cac
16 6 1 7 7 3 2 3 8 0 2 6 6 3 4 8 4 2
cag cat cca ccc ccg cct cga cgc cgg cgt cta ctc ctg ctt gaa gac gag gat
2 1 4 1 1 2 2 0 0 1 1 3 3 2 2 1 5 3
gca gcc gcg gct gga ggc ggg ggt gta gtc gtg gtt taa tac tag tat tca tcc
5 1 0 2 4 0 1 3 2 0 2 3 11 4 8 11 2 4
tcg tct tga tgc tgg tgt tta ttc ttg ttt
1 1 8 4 6 3 4 4 8 9
> uco( rcds, index = "rscu")
aaa aac aag aat aca acc acg
1.8823529 0.9230769 0.1176471 1.0769231 1.8666667 0.8000000 0.5333333
act aga agc agg agt ata atc
0.8000000 3.6923077 0.0000000 0.9230769 2.5714286 1.0588235 0.5294118
atg att caa cac cag cat cca
1.0000000 1.4117647 1.3333333 1.3333333 0.6666667 0.6666667 2.0000000
ccc ccg cct cga cgc cgg cgt
0.5000000 0.5000000 1.0000000 0.9230769 0.0000000 0.0000000 0.4615385
cta ctc ctg ctt gaa gac gag
0.2857143 0.8571429 0.8571429 0.5714286 0.5714286 0.5000000 1.4285714
gat gca gcc gcg gct gga ggc
1.5000000 2.5000000 0.5000000 0.0000000 1.0000000 2.0000000 0.0000000
ggg ggt gta gtc gtg gtt taa
0.5000000 1.5000000 1.1428571 0.0000000 1.1428571 1.7142857 1.2222222
tac tag tat tca tcc tcg tct
0.5333333 0.8888889 1.4666667 0.8571429 1.7142857 0.4285714 0.4285714
tga tgc tgg tgt tta ttc ttg
0.8888889 1.1428571 1.0000000 0.8571429 1.1428571 0.6153846 2.2857143
ttt
1.3846154
> uco( rcds, as.data.frame = FALSE, NA.rscu = NA)
aaa aac aag aat aca acc acg act aga agc agg agt ata atc atg att caa cac
16 6 1 7 7 3 2 3 8 0 2 6 6 3 4 8 4 2
cag cat cca ccc ccg cct cga cgc cgg cgt cta ctc ctg ctt gaa gac gag gat
2 1 4 1 1 2 2 0 0 1 1 3 3 2 2 1 5 3
gca gcc gcg gct gga ggc ggg ggt gta gtc gtg gtt taa tac tag tat tca tcc
5 1 0 2 4 0 1 3 2 0 2 3 11 4 8 11 2 4
tcg tct tga tgc tgg tgt tta ttc ttg ttt
1 1 8 4 6 3 4 4 8 9
> uco( rcds, as.data.frame = TRUE, NA.rscu = NA)
AA codon eff freq RSCU
aaa Lys aaa 16 0.068669528 1.8823529
aac Asn aac 6 0.025751073 0.9230769
aag Lys aag 1 0.004291845 0.1176471
aat Asn aat 7 0.030042918 1.0769231
aca Thr aca 7 0.030042918 1.8666667
acc Thr acc 3 0.012875536 0.8000000
acg Thr acg 2 0.008583691 0.5333333
act Thr act 3 0.012875536 0.8000000
aga Arg aga 8 0.034334764 3.6923077
agc Ser agc 0 0.000000000 0.0000000
agg Arg agg 2 0.008583691 0.9230769
agt Ser agt 6 0.025751073 2.5714286
ata Ile ata 6 0.025751073 1.0588235
atc Ile atc 3 0.012875536 0.5294118
atg Met atg 4 0.017167382 1.0000000
att Ile att 8 0.034334764 1.4117647
caa Gln caa 4 0.017167382 1.3333333
cac His cac 2 0.008583691 1.3333333
cag Gln cag 2 0.008583691 0.6666667
cat His cat 1 0.004291845 0.6666667
cca Pro cca 4 0.017167382 2.0000000
ccc Pro ccc 1 0.004291845 0.5000000
ccg Pro ccg 1 0.004291845 0.5000000
cct Pro cct 2 0.008583691 1.0000000
cga Arg cga 2 0.008583691 0.9230769
cgc Arg cgc 0 0.000000000 0.0000000
cgg Arg cgg 0 0.000000000 0.0000000
cgt Arg cgt 1 0.004291845 0.4615385
cta Leu cta 1 0.004291845 0.2857143
ctc Leu ctc 3 0.012875536 0.8571429
ctg Leu ctg 3 0.012875536 0.8571429
ctt Leu ctt 2 0.008583691 0.5714286
gaa Glu gaa 2 0.008583691 0.5714286
gac Asp gac 1 0.004291845 0.5000000
gag Glu gag 5 0.021459227 1.4285714
gat Asp gat 3 0.012875536 1.5000000
gca Ala gca 5 0.021459227 2.5000000
gcc Ala gcc 1 0.004291845 0.5000000
gcg Ala gcg 0 0.000000000 0.0000000
gct Ala gct 2 0.008583691 1.0000000
gga Gly gga 4 0.017167382 2.0000000
ggc Gly ggc 0 0.000000000 0.0000000
ggg Gly ggg 1 0.004291845 0.5000000
ggt Gly ggt 3 0.012875536 1.5000000
gta Val gta 2 0.008583691 1.1428571
gtc Val gtc 0 0.000000000 0.0000000
gtg Val gtg 2 0.008583691 1.1428571
gtt Val gtt 3 0.012875536 1.7142857
taa Stp taa 11 0.047210300 1.2222222
tac Tyr tac 4 0.017167382 0.5333333
tag Stp tag 8 0.034334764 0.8888889
tat Tyr tat 11 0.047210300 1.4666667
tca Ser tca 2 0.008583691 0.8571429
tcc Ser tcc 4 0.017167382 1.7142857
tcg Ser tcg 1 0.004291845 0.4285714
tct Ser tct 1 0.004291845 0.4285714
tga Stp tga 8 0.034334764 0.8888889
tgc Cys tgc 4 0.017167382 1.1428571
tgg Trp tgg 6 0.025751073 1.0000000
tgt Cys tgt 3 0.012875536 0.8571429
tta Leu tta 4 0.017167382 1.1428571
ttc Phe ttc 4 0.017167382 0.6153846
ttg Leu ttg 8 0.034334764 2.2857143
ttt Phe ttt 9 0.038626609 1.3846154
>
This is the output from the computation
First of all, store the output of the function in a variable, e.g.:
results_final_v2 <- uco( rcds, index = "freq")
For the names of your variables, you can use any letters A-Z, a-z, 0-9, underscore. Best avoid special characters.
Now you will see the results in the R environment, and other functions will be able to use it. It won't show in the console automatically, but you can still view it by just typing the name of your variable, e.g. results_final_v2.
Now to export your data. To export it to other R users:
save(results_final_v2, file='export1.RData')
You can specify multiple variable names, if you want to export multiple variables into one file.
To export to CSV (for Excel):
write.csv(results_final_v2, file='export1.csv'
In Excel, you import the resulting .csv file through 'Import' or 'Data > From Text'. For European users, write.csv2() usually works better.
There are also methods to write to an xlsx file directly or copy the data to the clipboard.