User: marcusanaymik

gravatar for marcusanaymik
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United States
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1 month, 3 weeks ago
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3 years, 11 months ago
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Posts by marcusanaymik

<prev • 7 results • page 1 of 1 • next >
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Affymetrix A/B allele coding to reference 'forward' allele coding manual conversion
... I have a ped file with genotypes from the Genome-Wide Human SNP Array 6.0 array in their native A/B format. I need to convert these to the standard forward coding used by dbsnp and hg19. Does anyone have experience doing this? ...
array allele coding snp affymetrix genotypes written 6 months ago by marcusanaymik10 • updated 6 months ago by Biostar ♦♦ 20
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Number of reference sequence contigs in sam/bam header does not match the number in my fasta
... I created a de novo assembly fasta (masked) which I then used to align the fastq sequences to. I noticed that when building the bowtie 2 reference index for the assembly there were many sequences that were all N's (662,820 to be exact) which I expected from the masking. After alignment I did a grep ...
fasta bowtie2 contig sam bam written 2.4 years ago by marcusanaymik10 • updated 2.4 years ago by Brian Bushnell16k
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vcftool negative relatedness values for family members
... I have ran the vcftools relatedness2 analysis on a few families data and some families produce positive relatedness phi scores and some families produce negative phi scores. In the range of + or - [0.1 - 0.3] for child-parents. Is the + - irrelevant? ...
pedigree kinship qc vcftools written 3.2 years ago by marcusanaymik10 • updated 6 months ago by Biostar ♦♦ 20
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Comment: C: RnBeads Pairwise Differential Methylation Tables
... Sorry, I should have replied directly to this. My reply is below. ...
written 3.4 years ago by marcusanaymik10
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Answer: A: RnBeads Pairwise Differential Methylation Tables
... I miss understood that. By pairwise I mean a pair of samples not pair of groups, so strictly 1 case vs 1 control. In my case an affected child vs an unaffected mother. When I tried to put just two samples in the sample_annotation file it does not run at all, it would not run with three samples eithe ...
written 3.4 years ago by marcusanaymik10
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RnBeads Pairwise Differential Methylation Tables
... I am trying to run the differential methylation portion of RnBeads with pairwise.all set. It seems to recognize the pairwise option but I can't find any trace of pairwise data/tables, the group analysis completed however. > diffmeth=rnb.execute.computeDiffMeth(rnb.set,cmp.cols,region.ty ...
pairwise methylation tool rnbeads written 3.4 years ago by marcusanaymik10
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RCircos Heatmap Colors
... Hi I am new to using RCircos and was wondering if anyone knows how to change the heatmap colors? I see there is a function to view the other built-in color ranges but not to set them. Thanks, Marcus ...
R plot colors rcircos heatmap written 4.0 years ago by marcusanaymik10 • updated 2.4 years ago by jason830120

Latest awards to marcusanaymik

Popular Question 5 months ago, created a question with more than 1,000 views. For RCircos Heatmap Colors
Supporter 5 months ago, voted at least 25 times.
Popular Question 16 months ago, created a question with more than 1,000 views. For RCircos Heatmap Colors
Popular Question 2.0 years ago, created a question with more than 1,000 views. For RCircos Heatmap Colors

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