User: veronico

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veronico60
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Posts by veronico

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Comment: C: mutate function dropping row names in r
... Thank you so much! This was super helpful! ...
written 5 months ago by veronico60
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Forum: Annotation for WGBS
... Hi everyone, Does anyone have a good recommendation for annotating genes, gene bodies, enhancers, promoters, CpG islands, etc for WGBS data (just CpGs)? I want to understand the affect of my drug over a span of time and how it affects DNA methylation by looking at various annotations, but I dont r ...
forum next-gen written 5 months ago by veronico60
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mutate function dropping row names in r
... Hi everyone, Does anyone know how to fix this: I am using the following code to create certain groupings, but doing so changes my row names to numbers. Is there a way to avoid this, please? table5[] <- death%>% mutate(Group = case_when( Mean > 0 ~ "1", Mean < 0 & Mean ...
R written 9 months ago by veronico60 • updated 9 months ago by zx87549.6k
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Comment: C: Cox regression survival analysis - using a panel of genes with TCGA
... the panel of genes came from some analysis from my lab. I included only 4 genes just to simplify it. I get the following graph: https://flic.kr/p/2hvMBui ...
written 11 months ago by veronico60
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Comment: C: Cox regression survival analysis - using a panel of genes with TCGA
... Sorry, needed to put the rest of the code in another comment 'cuz I reached the max of characters. # and days last follow up here we take the most recent which is the max number ind_keep <- grep('days_to_last_followup',colnames(clinical)) fl <- as.matrix(clinical[,ind_kee ...
written 11 months ago by veronico60
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Comment: C: Cox regression survival analysis - using a panel of genes with TCGA
... Hi Kevin, Thank you so much for answering! I will include my whole code. Basically, I got mRNA-seq data from TCGA (Fire Browser). I followed the instructions from this link (https://www.biostars.org/p/153013/). However, this looks at single genes at a time. So, thankfully the survival package incl ...
written 11 months ago by veronico60
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Cox regression survival analysis - using a panel of genes with TCGA
... I am using the survival package in R and have a panel of genes that I want to use to determine if these group of genes affect survival. I towards the end and want to produce the graph, but I keep getting one line graph with what appears confidence lines flanking it. Has anyone used it for a panel ...
tcga panel survival written 11 months ago by veronico60 • updated 11 months ago by Kevin Blighe65k
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Comment: C: TCGA survival analysis using >100 genes
... Ok, thank you. I'll look into `apply` ...
written 13 months ago by veronico60
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Comment: C: TCGA survival analysis using >100 genes
... for each gene? My apologies I am not following. Would this work if I have a panel of a >100 genes that I want to investigate together? ...
written 13 months ago by veronico60
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TCGA survival analysis using >100 genes
... Hi everyone, I hope everyone is doing well! I was wondering if anyone knew how to do survival analysis by using a panel of >100 genes? I have a list of genes I am interested in (>100 genes) and I want to find these list of genes that are down regulated from RNA seq data from TCGA (preferably ...
many tcga rna-seq survival written 13 months ago by veronico60 • updated 13 months ago by h.mon31k

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