3
votes
Filtering columns from large file based on a column list
It's really just count[,col$V1]. Please learn about basic subsetting of columns and rows, it's simple yet powerful.
- 1,078
3
votes
Filtering columns from large file based on a column list
You can save time and memory by preprocessing your file before loading it into R.
Use miller toolkit to manipulate csv or tab-delimited files using column names.
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1
vote
PANTHER FUNCTIONAL CLASSIFICATION in R
One approach is to get the gene's sequence (DNA/AA) and use the interproscan API (e.g., https://www.ebi.ac.uk/Tools/common/tools/help/index.html?tool=iprscan5) with the httr2 library in R to POST ...
- 11
1
vote
1
vote
biomarRT conversion of symbols
My background in coding is more extensive in Python. If you have Python skills, I can say for sure, use the Bioservices library:
from bioservices import BioMart
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1
vote
Intepreting and applying ordinal logistic regression coefficients to calculate probabilities?
Its a while since I've done GLM because ML is the method of choice.
Question1 Yes multi-linear regression is an approximate description of GLM.
Generally the weights simply mean whether a feature is ...
M__♦
- 11.9k
1
vote
1
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Mendelian randomization
I understand linkage disequilibrium (LD) versus panmixia, which the technical term for Mendelian randomisation and for humans PLINK is a population package. The best outcome is a correlation between ...
M__♦
- 11.9k
1
vote
error in downloading the annotation of sequences on NCBI
You could use the tryCatch function to handle inputs that throw an error. A good example on how to write them can be found here. Though the message indicates it's a ...
- 111
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