User: Sam

gravatar for Sam
Sam3.3k
Reputation:
3,270
Status:
Trusted
Location:
New York
Last seen:
1 week, 2 days ago
Joined:
9 years, 5 months ago
Email:
c***********@gmail.com

Posts by Sam

<prev • 472 results • page 1 of 48 • next >
1
vote
1
answer
211
views
1
answers
Comment: C: How to understand Instance and Array in UKB phenotype data
... have never worked with this phenotype so I don't have any idea. Their [document][1] on this also isn't very clear. If I have to guess based on information from the note section, which stated: The Bike Test consists of many phases. A phase is generally divided into number of stages. At various points ...
written 23 days ago by Sam3.3k
3
votes
1
answer
122
views
1
answers
Answer: A: Error: object not found - Second loop
... what you want might be instead f <- read.table(file = "GeneExpressionDataset_normalized.tsv", sep="\t", header=TRUE) wt <- apply(f[,2:11], 1, mean) TherA <- apply(f[,22:31], 1, mean) (I am guessing that you are looking for the mean of each group for each row) ...
written 8 weeks ago by Sam3.3k
1
vote
1
answer
194
views
1
answers
Comment: C: filtering column based on column header from a file
... I am not sure what your identifier column name is, but assuming it is "ID" you can do col <- c("ID", col) And continue ...
written 10 weeks ago by Sam3.3k
2
votes
1
answer
194
views
1
answers
Answer: A: filtering column based on column header from a file
... Assuming you are trying to extract the columns by column names, you can do the following with data.table library(data.table) col <- unlist(fread("column.txt", header=F)) count <- fread("count.txt") extracted <- count[,col, with=F] If you don't have data.table install, you ...
written 10 weeks ago by Sam3.3k
2
votes
2
answers
180
views
2
answers
Answer: A: Replacing NA values of a column using values from another column
... If you have data.table installed, and assuming your data is stored in `dat` library(data.table) dat <- as.data.table(dat) dat[is.na(H1), H1:=H2] should do ...
written 3 months ago by Sam3.3k
0
votes
0
answers
684
views
0
answers
Comment: C: Plot GWAS p value distribution for multiple traits
... From the sound of it, you seems to be doing a phewas study. This package might be helpful https://pubmed.ncbi.nlm.nih.gov/24733291/ ...
written 3 months ago by Sam3.3k
0
votes
2
answers
182
views
2
answers
Answer: A: Re-joining sample ID's and snp information from bgen files for analysis in R
... You can try to convert the BGEN file into a VCF or uncompressed GEN fille and extract the SNPs / samples at the same time using QCTools developed by BGEN's author. ...
written 3 months ago by Sam3.3k
1
vote
1
answer
180
views
1
answers
Answer: A: PRSice: how to obtain exact list of SNPs used for PRSice.best
... Use `--print-snp` which will generate a ***output prefix***.snp file. This file contain all the post-clump SNPs and their p-value. You can then filter out the SNPs included in the best score by filtering according to the p-value threshold ...
written 3 months ago by Sam3.3k
0
votes
2
answers
2.3k
views
2
answers
Comment: C: Fold change instead of expression (intensity values) in co-expression network?
... Unfortunately, that was almost 5 years ago and I really have no memory of what that link was. Though I guess it might be something related to Network analyzer from UCSF? Something like http://www.cgl.ucsf.edu/home/scooter/CSB/Network_Analyzer_Handout.pdf ...
written 3 months ago by Sam3.3k
0
votes
2
answers
405
views
2
answers
Comment: C: How to perform GWAS using BOLT-LMM iteratively for many phenotypes in bash
... That depends on your job submission system ...
written 4 months ago by Sam3.3k

Latest awards to Sam

Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Tutorial (How to analyze) on Whole Exome sequencing. Common Errors. Best Practic
Scholar 10 weeks ago, created an answer that has been accepted. For A: Annovar: how to update sequence length based on deletion size
Scholar 4 months ago, created an answer that has been accepted. For A: Annovar: how to update sequence length based on deletion size
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Tutorial (How to analyze) on Whole Exome sequencing. Common Errors. Best Practic
Appreciated 5 months ago, created a post with more than 5 votes. For A: High Sequence Duplication levels in FastQC
Scholar 5 months ago, created an answer that has been accepted. For A: Gene regulatory networks from RNA-seq data
Scholar 6 months ago, created an answer that has been accepted. For A: Gene regulatory networks from RNA-seq data
Scholar 7 months ago, created an answer that has been accepted. For A: Gene regulatory networks from RNA-seq data
Scholar 9 months ago, created an answer that has been accepted. For A: Gene regulatory networks from RNA-seq data
Appreciated 9 months ago, created a post with more than 5 votes. For A: High Sequence Duplication levels in FastQC
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Gene regulatory networks from RNA-seq data
Epic Question 13 months ago, created a question with more than 10,000 views. For Normalization Of Rna Sequencing Counts (By Ercc / Gene Length)
Scholar 13 months ago, created an answer that has been accepted. For A: Gene regulatory networks from RNA-seq data
Scholar 15 months ago, created an answer that has been accepted. For A: Gene regulatory networks from RNA-seq data
Scholar 16 months ago, created an answer that has been accepted. For A: Gene regulatory networks from RNA-seq data
Popular Question 19 months ago, created a question with more than 1,000 views. For Method for analyzing Targeted re-sequencing based on Ligation Mediated PCR?
Appreciated 24 months ago, created a post with more than 5 votes. For A: High Sequence Duplication levels in FastQC
Student 2.3 years ago, asked a question with at least 3 up-votes. For Interpretation Of Differential Exon Usage Results
Great Question 2.3 years ago, created a question with more than 5,000 views. For Piping Markduplicates
Popular Question 2.9 years ago, created a question with more than 1,000 views. For High Kmer Content in middle of the read
Good Answer 3.1 years ago, created an answer that was upvoted at least 5 times. For A: High Sequence Duplication levels in FastQC
Commentator 3.2 years ago, created a comment with at least 3 up-votes. For C: difference between assembly hg19 and GRCh37
Appreciated 3.7 years ago, created a post with more than 5 votes. For A: High Sequence Duplication levels in FastQC
Popular Question 3.7 years ago, created a question with more than 1,000 views. For High Kmer Content in middle of the read
Popular Question 4.1 years ago, created a question with more than 1,000 views. For RNA Sequencing Pooling design and statistic analysis

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1905 users visited in the last hour
_