User: Yadav Sapkota

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Yadav Sapkota130
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Posts by Yadav Sapkota

<prev • 13 results • page 1 of 2 • next >
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Overlapping ROC plots
... Hello group, I am trying to compare the classification accuracies of multiple classifiers using ROC curves. I have created multiple ROC plots for each of these classifiers but I am looking for a single graph where I can overlay each of these individual ROC plots. Does anyone know anything about cre ...
classification roc graph written 6.9 years ago by Yadav Sapkota130
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Calculate heterozygosity % using SNP genotype data
... Hello, I am trying to validate few LOH regions using SNP genotype data. I am assuming that if it is a LOH, it will contain predominantly homozygous genotypes. For simplicity, I chose 15 SNPs per ~70 kb LOH region. Now I need to calculate the heterozygosity for LOHs in each samples using genotype d ...
snp written 7.0 years ago by Yadav Sapkota130 • updated 6.9 years ago by Valerie Obenchain6.7k
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Comment: C: Query neighboring genes
... Hi, Many thanks for pointers. Actually everything worked fine when I tried to perform GO analysis for the genes which are within 20 KB upstream and 10 KB downstream of a given chromosomal region (CNV in my case) except GO analysis resulted in null. I used following scripts: source("http://biocond ...
written 7.0 years ago by Yadav Sapkota130
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GO analysis using chromosomal ranges
... Hi, Is there any tool or package that takes chromosomal ranges (instead of gene IDs) as input and performs GO analysis? Any help will be appreciated. --Yadav [[alternative HTML version deleted]] ...
go written 7.0 years ago by Yadav Sapkota130 • updated 7.0 years ago by Martin Morgan ♦♦ 23k
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Comment: C: Query neighboring genes
... Hi, I tried this function and it works fine for me however, I could not find any option to define the upstream and downstream size while looking for neighboring genes. For example, I wanted to only query genes that are located 100 KB upstream and 50 KB downstream from a chromosomal range. Any hint ...
written 7.0 years ago by Yadav Sapkota130
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Query neighboring genes
... Hi, Is there any tool or package that can query neighboring genes (lets say 100 KB upstream and downstream) of a specific chromosomal range (chr1:100-200)? I have thousands of these chromosomal ranges. You help will be greatly appreciated. Regards, Yadav Sapkota Uni of Alberta [[alternat ...
written 7.0 years ago by Yadav Sapkota130 • updated 7.0 years ago by Julie Zhu4.0k
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GO analysis for CNVs
... Hi, I have some candidate CNVs (with chromosomal start and end position known) but these are not in the gene regions but located upstream or downstream of some genes. Is there any tool or R package where I can use CNV information (as input) and use some options that will allow me to conduct the GO ...
go written 7.0 years ago by Yadav Sapkota130 • updated 7.0 years ago by Julie Zhu4.0k
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Gene-gene interaction analysis
... Hi, I am looking for a tool or R package that can take SNPs or DE genes with their p-values and build a graphical representation showing possible gene-gene interactions using prior knowledge from protein interactions databases such as KEGG with some scores for the interaction. I know this can be do ...
cancer written 7.1 years ago by Yadav Sapkota130 • updated 7.1 years ago by Tengfei Yin420
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Comment: C: Manhattan plot for CNVs association results
... Sure....will wait for your e-mail... --Yadav On Tue, Apr 3, 2012 at 2:06 PM, Tengfei Yin wrote: > > > On Tue, Apr 3, 2012 at 2:50 PM, Yadav Sapkota wrote: > >> Hi Tengfei, >> >> Thanks for the info. It worked so far using the following code: >> >> source ...
written 7.1 years ago by Yadav Sapkota130
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Comment: C: Manhattan plot for CNVs association results
... Hi Tengfei, Thanks for the info. It worked so far using the following code: source("http://bioconductor.org/biocLite.R") biocLite("GenomicRanges") library(GenomicRanges) mydata=read.table('C:/......Book1.csv', header=T, sep=',') attach(mydata) gr.cnv=GRanges(Chr, IRanges(Start, Stop), pvalue=mydat ...
written 7.1 years ago by Yadav Sapkota130

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