User: cpad0112
cpad0112 • 7.7k
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Posts by cpad0112
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... some example data would help @OP ...
written 20 hours ago by
cpad0112 • 7.7k
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2
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92
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... querying b151 dbsnp vcf didn't yield any results.
$ tabix ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/VCF/All_20180418.vcf.gz 1:45194429-45194431
...
written 20 hours ago by
cpad0112 • 7.7k
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107
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... All OP's fasta files seem to start with `xa` (from the description in OP). To be safe, it may be better for OP to restrict the code either with `x` or `xa` (some thing like `ls x*.txt` or `ls xa*.txt`) ...
written 1 day ago by
cpad0112 • 7.7k
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85
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... https://www.biostars.org/u/45426/ 39 entry in geneID1 seems to be problematic and try removing it, Try running for 39 and it will fail:
geneSim(geneID1=geneID1[39], geneID2 = geneID2, measure ="Resnik", combine = "BMA",semData=meshdata)
and
geneSim(geneID1=geneID1[40], geneID2 = geneID2, ...
written 1 day ago by
cpad0112 • 7.7k
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159
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... https://gist.github.com/cpad0112/22e551eaa6a6508fc9b6345e9aac8162
Fasta files must be flattened (`seqkit seq -w 0 input fasta` for flattening fasta) ...
written 1 day ago by
cpad0112 • 7.7k
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68
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... GenomicDataCommons v1.2.0 has `as.data.frame.GDCResults` function. Try `help(package = GenomicDataCommons)` to see the functions. I think there is basic functionality issue. Try `GenomicDataCommons::status()` ...
written 1 day ago by
cpad0112 • 7.7k
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... @OP: Try this. tagging the author: https://www.biostars.org/u/287/
library("GenomicDataCommons")
test = cases() %>% filter(~ project.project_id=='TCGA-CHOL') %>% results(n=10) %>% as.data.frame())
Unfortunately, I am not able to connect to gdc server.
...
written 1 day ago by
cpad0112 • 7.7k
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68
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... https://www.rdocumentation.org/packages/GenomicDataCommons/versions/1.3.1/topics/as.data.frame.GDCResults
copy/pasted from webpage:
expands = c("diagnoses","diagnoses.treatments","annotations", "demographic","exposures")
head(cases() %>% expand(expands) %>% results() %>% as.da ...
written 1 day ago by
cpad0112 • 7.7k
0
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108
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... with [datamash][1]. Added an extra row to check for sorting.
$ sed 's/%//g' test.txt | datamash -sfg 1 max 4| cut --complement -f5 | sed 's/$/%/g'
sample1 200000 120000 90%
sample2 200000 190000 95%
$ cat test.txt
sample1 200000 120000 60%
sample1 200000 115000 57.5%
...
written 2 days ago by
cpad0112 • 7.7k
1
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5
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140
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5
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... echo "AA GG TG CC" | sed 's/\s//g;s/./& /g'
or
echo "AA GG TG CC" | sed 's/./& /g' | tr -s " "
A A G G T G C C
...
written 3 days ago by
cpad0112 • 7.7k
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