Hello everyone
I hope you are safe and good
I have genomic ranges below in which minor allele = 0
means loss of Heterozygosity
. (LOH)
Chr start end
1 10583 863511
1 12841835 12854479
1 17231299 17232877
1 120380739 142540462
1 142540484 142684781
1 142685823 143462598
1 143466928 143533092
1 143534046 144064964
1 145079160 145110146
1 145121086 145400508
I have another data frame like below where I have position of mutations in each genes
> head(mut[,c(2:7)])
Chromosome Start_Position End_Position Reference_Allele Tumor_Seq_Allele2
1 chr1 89616151 89616151 - T
2 chr6 51909815 51909815 A -
3 chr16 20556547 20556547 - G
4 chr17 66992092 66992092 - A
5 chr20 13251339 13251339 - T
6 chr20 35929770 35929771 TC -
Hugo_Symbol
1 GBP7
2 PKHD1
3 ACSM2B
4 ABCA9
5 ISM1
6 MANBAL
>
I want to know which genes also have los of Heterozygosity based on the first data frame
Thank you for any help
Thank you
Sorry one question: If
gr1
comes from my first data frame (which containing range withminor allele =0
) then what I should put infeature
column of that?For
gr2
if I am not wrong, gene column contains gene symbols I am proving in the second data frame with mutationsI am wondering because when creating my gr objects I got this
My code is just providing an example. For your data, you just need 'chr', 'start', 'end'.
Again, my code is just providing an example. You can have any amount of extra columns (other than 'chromosome', 'start', and 'end') that contain any information.
----------
The 'vector memory' error means that you do not have enough RAM. On which computer are you running the code and how much RAM does it have? Also, which version of R, and what ids the size of your gr1 and gr2?
Thank you
My data is for 15 patients
Thank you, but, how much RAM does your computer have?; how many regions are in your input files?; which commands are you running?
RAM is
8 GB 1867 MHz DDR3
Sorry I don't know how many regions I have
I have followed your commands
Sorry, even by googling I can not figure out why I have to overlap regions of genome with
minor allele = 0
withregions of genomes with mutation
Actually in my understanding, LOH is losing one parental allele
But why we need to find a gene with both copy number loss and mutation
To be honest I can not understand the intuition and logic behind this story
Hello again. It seems that your questions are now more general. This website is designed for questions about technical issues relating to Bioconductor packages. I wish you the best in your project.
Sorry @Kevin Blighe
I have used your instruction like below
I need the output for clonality analysis but I am seeing likely I have redundancy and reputation after merging copy number and variant data
Is it normal or I am doing something wrong?