User: haneenih7

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haneenih760
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PhD student

Posts by haneenih7

<prev • 37 results • page 1 of 4 • next >
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Comment: C: Order file based on another file
... Thank you! Your hint was helpful! `inner_join` didn't produce the same order as in file 2; However, `left_join` worked !! usage: `left_join(data.frame(V1=file2),file1,by="V1")` ...
written 28 days ago by haneenih760
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Order file based on another file
... Hello I have two files, I want to order the first file based on the second file. Example here the first file: 0.448032 0.551968 CM04487 Benin 1.383333333 10.5 2 0.53082 0.46918 CM04489 Benin 0.783333333 10.4 1 0.9999 1.00E-04 CM06501 Burkina Faso -3.083333333 13.36666667 1 0.9328 ...
R bash written 28 days ago by haneenih760
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Answer: A: Saving high quality image in R
... Controlling the width and height solved the problem: tiff("test.tiff", units="cm", width=20, height=15, res=300, pointsize=6) ...
written 4 weeks ago by haneenih760
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Saving high quality image in R
... Hello all, I am trying to save image in R with resolution= 300 in tiff or png formate I have this code, but for some reason, the image is not saved in the directory tiff("test.tiff", units="cm", width=5, height=7, res=300, pointsize=6) ggplot(data=a, aes(x=BIN_START, y=1)) + facet_gri ...
R written 4 weeks ago by haneenih760 • updated 4 weeks ago by i.sudbery6.6k
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Answer: A: Output the results of samtools flagstat of 180 bam files in one text file
... One option is to concatenate all files together after the for loop finishes. grep "" *.txt > all_files This won't give a 'header', but it prefixes every line with the filename. ...
written 4 weeks ago by haneenih760
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Output the results of samtools flagstat of 180 bam files in one text file
... Hello, I have 180 bam files that I wanna see the mapping rate. I am running a for loop in files, and using ***samtools flagstat*** to get the stats, I want to have the output results for all the files in one text file with the file name so it would be something like this: >M883.rgroup.bam ...
genome alignment for loop shell written 4 weeks ago by haneenih760 • updated 4 weeks ago by Pierre Lindenbaum125k
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Comment: C: How to check how much loading each SNP had on the first or second principal comp
... Thanks a lot! I know it's possible with plink and adegenet R package But because my PCA was produced by the pca function from the R package LEA. Then I would look for the loadings using the produced files by this function ...
written 9 weeks ago by haneenih760
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How to check how much loading each SNP had on the first or second principal component
... Hello, I did PCA analysis using pca function from the LEA r package It produces these files: > eigenvalue file: genotypes_cultivated.eigenvalues > eigenvector file: genotypes_cultivated.eigenvectors > standard deviation file: genotypes_cultivated ...
pca snp written 9 weeks ago by haneenih760 • updated 9 weeks ago by chrchang5236.3k
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Comment: C: Run R script on 100 files using for loop
... Thank you! but I am getting this error: Error in write.geno(wind, the_dir, basename(file)) : unused argument (basename(file)) from the function write.geno ...
written 10 weeks ago by haneenih760
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Run R script on 100 files using for loop
... Hello, I need to run this small R script from LEA r package for 100 files: mb10 <- fread("wind43.geno") # this is the file after replacing -1 by 9 write.geno(mb10, "genotypes_chr09A_10mb.geno") output = geno2lfmm("wind43.geno") I think one option is to do for loop, I have written ...
R written 10 weeks ago by haneenih760

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