User: kbaitsi

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Posts by kbaitsi

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Answer: C: Combine conditions between two matrices of the same size
... For anyone who might face the same problem since the matrices are of the same size. which( ( (logFC>=1) | (logFC <= -1) ) & (pvadj<=0.05), arr.ind = TRUE, useNames = TRUE) ...
written 10 days ago by kbaitsi0
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Comment: C: Combine conditions between two matrices of the same size
... I also tried duplicated hh<-duplicated(rbind(con1,con2)) hh1<-as.matrix(hh) but the outcome is just the rowanmes, not the entire row. ...
written 10 days ago by kbaitsi0
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Combine conditions between two matrices of the same size
... I have produced two matrices of the same size using R, from a microarray tsv file. One matrix with the log2FC of every gene in each of the 5 conditions and one matrix with the p.adjusted value of every gene in each of the 5 conditions. My goal is to find the genes that satisfy both the conditions lo ...
R log2fc padjval conditions written 10 days ago by kbaitsi0
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Comment: C: Error: object not found - Second loop
... Yes, this was my intention. Your way seems more suitable. Thank you! ...
written 11 days ago by kbaitsi0
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Error: object not found - Second loop
... I have a tsv file with 61 columns and 18703 lines. I have written the following code: f<-read.table(file = "GeneExpressionDataset_normalized.tsv", sep="\t", header=TRUE) m<-as.data.frame(f) m for (i in 1:nrow(m)){ wt[i]<-c(sum(m[c(i:i),c(2:11)]))/10 } wt ...
R loop written 11 days ago by kbaitsi0 • updated 11 days ago by Sam3.3k
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Comment: C: How can I create a new fasta file after modifying an existing fasta file?
... The original fasta file is called histone4.fa. After I have generated the new sequence(new hist) I write `write.fasta(newhist, names = names("histone4.fa"), file.out = "histone4.fa", open = "a")` and a new line is added to my open fasta file. If I write `write.fasta(newhist, names = names("histone4. ...
written 16 days ago by kbaitsi0
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How can I create a new fasta file after modifying an existing fasta file?
... I have a fasta file with 10 protein sequences. Using R I generate a new protein sequence and using write.fasta I insert the new sequence in the original file. Is there a way to create a new fasta file with a new name containing the 11 sequences? Basically I need to "save as". ...
write.fasta R new_fasta_file written 16 days ago by kbaitsi0
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Comment: C: Similarity matrix to distance matrix for protein sequences
... I have used the pairwise alignment function and a blosum subtitution matrix. Thanks a lot for your time and answer. ...
written 17 days ago by kbaitsi0
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Comment: C: Similarity matrix to distance matrix for protein sequences
... Thank you for your answer, sim2dist does what you wrote in the first bullet. I was just wondering if there is a preferable way when it comes to protein sequences or it doesn't matter? ...
written 17 days ago by kbaitsi0
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Similarity matrix to distance matrix for protein sequences
... I have used R to calculate a similarity matrix for 11 proteins (histones) from a fasta file. Then I need to turn the similarity matrix into a distance matrix in order to use it in **hclust**. I have used **sim2dist** and also **dist** with all methods (euclidean, maximum, manhattan, canberra, binary ...
similarity protein sequences distance R written 17 days ago by kbaitsi0

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