I am a new hand in the data analysis. Now I have the alignment results in .txt file, which includes subject sequence, pattern sequence, and score, as below:
subject: [1] AACGAACGCTGGCGGCATGCCTAACACATGCAAGT...GAAGTCGTAACAAGGTAGCCGTAGGGGAACCTGC
score: 3031.58
Global PairwiseAlignmentsSingleSubject (1 of 1)
pattern: [1] AACGAACGCTGGCGGCATGCCTAACACATGCAAGT...GAAGTCGTAACAAGGTAGCCGTAGGGGAACCTGC
subject: [1] AATGAACGCTGGCGGCATGCCTAACACATGCAAGT...GAAGTCGTAACAAGGTAGCCGTAGGGGAACCTGC
score: 2502.837
I plan to sort the score value for each aligned sequence and save the sorted scores in .txt files. I tried sort(), order() in R but didn't work. Could you please give me some suggestions or advice?
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written
by
LakeWind •
1 answer
Assuming your file is loaded as a dataframe, you could give this a try (how exactly did you use order() on your data? (Could you provide the actual code you used?):
df_ordered <- df[order(df[,"score"], decreasing = TRUE), ]
This should sort your dataframe in decreasing order based on the score (make sure "score" is also the column header here). If you prefer an ascending order, just remove the "decreasing" option or set it to false.
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Could you update your post with expected output?