User: Konstantinos Yeles

Reputation:
20
Status:
New User
Location:
University of Salerno, Salerno, Italy
Scholar ID:
Google Scholar Page
Last seen:
1 week, 5 days ago
Joined:
4 years, 2 months ago
Email:
y*****************@gmail.com

PhD student

Posts by Konstantinos Yeles

<prev • 74 results • page 1 of 8 • next >
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Comment: C: Understanding group_by, reduce_ranges,
... By "manually way" I mean something to use like apply or map to be done for each of the samples instead of writing for each sample `rep_1_counts = mean(rep_1_counts, na.rm = TRUE)`, but in real data, it is very time consuming (just using 3 samples it took 15mins). reduce_ranges_directed( ...
written 4 weeks ago by Konstantinos Yeles20
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Comment: C: Understanding group_by, reduce_ranges,
... I found the problem a bracket was missing... function(.) ifelseis.na(.), 0, .) %>% ^ function(.) ifelse/(is.na(.), 0, .) %>% Regarding `reduce_ranges_directed` is there a way to use the mean not manually? And when we have more seqlevels the correct way t ...
written 5 weeks ago by Konstantinos Yeles20
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Comment: C: Understanding group_by, reduce_ranges,
... For clarification (I don't know if it helps), I'm using a modified rocker container: [https://hub.docker.com/r/congelos/rocker_tidyverse_plus_de_pckages][1] [1]: https://hub.docker.com/r/congelos/rocker_tidyverse_plus_de_pckages ...
written 5 weeks ago by Konstantinos Yeles20
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Comment: C: Understanding group_by, reduce_ranges,
... I tried to do it twice in clean sessions. But doesn't it produce in your code an : > unexpected token ' ) ' > unexpected token ' %>% ' close to the line : `function(.) ifelseis.na(.), 0, .) ) %>%` plus the issue: Error in UseMethod("tbl_vars") : no applicable method ...
written 5 weeks ago by Konstantinos Yeles20
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Comment: C: Understanding group_by, reduce_ranges,
... more precisely i get this: r3 %>% + join_overlap_left_directed( rep1 ) %>% + join_overlap_left_directed( rep2 ) %>% + mutate(revmap = selfmatch(.)) %>% + dplyr::mutate_at(dplyr::vars(dplyr::starts_with('rep')), + function(.) ifelse ...
written 5 weeks ago by Konstantinos Yeles20
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Comment: C: Understanding group_by, reduce_ranges,
... Hello lee.s, thank you for your answer. I run the code but I get this: ans <- r3 %>% join_overlap_left_directed( rep1 ) %>% join_overlap_left_directed( rep2 ) %>% mutate(revmap = selfmatch(.)) %>% dplyr::mutate_at(dplyr::vars(dplyr::starts_with('rep')) ...
written 5 weeks ago by Konstantinos Yeles20
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Understanding group_by, reduce_ranges,
... Hello Bioconductor, I'm am trying to understand how the functions of group_by and reduce in plyranges package work. My purpose is to create a Granges object that has all the genomic ranges from BAM files and reduce them, to find the common / union in all samples. example: # toy samples taken ...
granges plyranges written 5 weeks ago by Konstantinos Yeles20 • updated 5 weeks ago by lee.s70
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Comment: C: Rsubread malloc(): memory corruption
... **Thank you very much!! I run it and this is what I get:** > alignmentmRNA <- align(index = path, + readfile1 = data, + #readfile2 = "./QC/QC_fastp/COLO205_CGATGTAT_L006_R2_001.fastq.gz", + type = "rna", + input_format = "FASTQ", + output ...
written 3 months ago by Konstantinos Yeles20
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Comment: C: Rsubread malloc(): memory corruption
... **I'm using** Virtual box 6.0.10 r132072(Qt5.6.1) **host machine:** CentOS Linux release 7.6.1810 (Core) NAME="CentOS Linux" VERSION="7 (Core)" ID="centos" ID_LIKE="rhel fedora" VERSION_ID="7" PRETTY_NAME="CentOS Linux 7 (Core)" ANSI_COLOR="0;31" CPE_NAME="cpe: ...
written 3 months ago by Konstantinos Yeles20
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Rsubread malloc(): memory corruption
... **Dear Bioconductor, I'm trying to use Rsubread in an Ubuntu virtual machine:** DISTRIB_ID=Ubuntu DISTRIB_RELEASE=18.04 DISTRIB_CODENAME=bionic DISTRIB_DESCRIPTION="Ubuntu 18.04.2 LTS" NAME="Ubuntu" VERSION="18.04.2 LTS (Bionic Beaver)" ID=ubuntu ID_LIKE=debian P ...
rsubread align malloc written 3 months ago by Konstantinos Yeles20 • updated 7 weeks ago by Gordon Smyth39k

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