User: rodolfo.peacewalker

Reputation:
0
Status:
New User
Last seen:
2 days, 11 hours ago
Joined:
1 month ago
Email:
r******************@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by rodolfo.peacewalker

<prev • 10 results • page 1 of 1 • next >
0
votes
1
answer
147
views
1
answers
Comment: C: Looping over list in R
... Finally, I resolved this issue. Some of my tibbles were empty. ...
written 28 days ago by rodolfo.peacewalker0
0
votes
1
answer
120
views
1
answers
Comment: C: Multiple plots using for loops in R
... Thanks for your help and suggestions. You were right, some of the tibbles inside the list were empty and, thus, caused a crash inside the loop. ...
written 28 days ago by rodolfo.peacewalker0
0
votes
1
answer
3.5k
views
1
answers
Comment: C: Multiple plots outputs using for loop in R
... I have a similar problem when I'm trying to generate multiple plots using a for loop. In this case, my GSEA results are stored as tibbles inside a list that looks like : > result $p1prnkpositional.db # A tibble: 68 x 9 pathway pval padj ES NES nMoreExtreme size l ...
written 29 days ago by rodolfo.peacewalker0
0
votes
2
answers
164
views
2
answers
Answer: C: Trim 3' ends from single-end reads
... Hi Maria! Did you try to use Trimmomatic? CROP and HEADCROP options allow you to trim your reads at 3' and 5' ends, respectively. With CROP option you specify the max length of your reads before trimming at 3' end. In your case 196 for the 220 bp reads or 176 for 200 bp reads. Then, use HEADCROP ...
written 4 weeks ago by rodolfo.peacewalker0
0
votes
1
answer
120
views
1
answer
Multiple plots using for loops in R
... Hi! I'm working with a GSEA analysis using the fGSEA package. In this case, the output of the GSEA analysis is stored in list that looks like: > result $p1prnkpositional.db # A tibble: 68 x 9 pathway pval padj ES NES nMoreExtreme size leadingEdge condition ...
R loop ggplot rna-seq written 4 weeks ago by rodolfo.peacewalker0 • updated 4 weeks ago by karl.stamm3.9k
0
votes
1
answer
147
views
1
answers
Comment: C: Looping over list in R
... Thanks for your help! I have run both codes but there is an error message as output. For the first one: > for (i in samps) { + pdf(paste0(i, ".pdf"), width = 10, height = 8) + print(barplot.NES(result[[i]])) + dev.off() + } Error: Faceting variables must have at lea ...
written 4 weeks ago by rodolfo.peacewalker0
0
votes
1
answer
147
views
1
answers
Comment: C: Looping over list in R
... rpolicastro, thanks for your help. The map function worked well! Now I have an issue related with plotting the data. I want to generate barplots to visualize the data in the tibbles, respect to NES value. I want to create multiple plots by running: samps <- as.vector(names(result)) for ...
written 4 weeks ago by rodolfo.peacewalker0
1
vote
1
answer
147
views
1
answer
Looping over list in R
... Hi! I have an issue related to looping over a list containing 54 dataframes (in this case, converted as tibble). The list content looks like: > result $`sample1prnk _ mir.db` # A tibble: 2,368 x 8 pathway pval padj ES NES nMoreExtreme size leadi ...
R loop list rna-seq written 4 weeks ago by rodolfo.peacewalker0 • updated 4 weeks ago by rpolicastro2.3k
0
votes
1
answer
111
views
1
answers
Comment: C: Looping in R to perform a GSEA analysis
... Thanks for your help and suggestions! It worked fine. ...
written 4 weeks ago by rodolfo.peacewalker0
1
vote
1
answer
111
views
1
answer
Looping in R to perform a GSEA analysis
... Hi! I need to run a GSEA analysis on distinct lists of pre-ranked DEG, as well as diverse lists of gene sets obtained from MSigDB. To run the analysis using one pre-ranked list and one gene set, the code is: fgsea_results <- fgsea(kegg.db, #Gene set b, ...
loops R rna-seq gsea written 4 weeks ago by rodolfo.peacewalker0

Latest awards to rodolfo.peacewalker

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2127 users visited in the last hour