User: Fersal

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Fersal20
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Posts by Fersal

<prev • 15 results • page 1 of 2 • next >
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(Closed) recoding genotype in R
... I am trying to re-code the following genotype data frame from biallelic code to "A", "B" code. corresponding to P1 and P2, respectively, which in turns correspond to the two parents. Please consider the following example. SNP P1 P2 in1 in2 in3 in4 M01 CC GG CC GG CC GG M02 TT CC TT TT C ...
R genotype recode written 6 months ago by Fersal20
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Comment: C: Counting the frequency of genotypes per row based on the calls of the first colu
... Effectively, that works!. But I realized it returns a `NA` instead of a value in the column `frqP1` for those rows that have at least one missing data (`NA`). Is there any way to avoid that? ...
written 6 months ago by Fersal20
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Counting the frequency of genotypes per row based on the calls of the first column in a data frame in R
... I have a genotype data frame in R similar to this ID P1 P2 in1 in2 in3 in4 M01 CC GG CC GG CC GG M02 TT CC TT TT CC TT M03 AA GG AA GG GG GG M04 CC GG CC GG CC GG M05 GG AA AA GG AA AA M06 CC GG CC GG CC CC I want to add a column with the frequencies of all the genotype ...
R genotype written 6 months ago by Fersal20 • updated 6 months ago by ATpoint16k
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Comment: C: Using variables into data frame names in R
... Thanks for your answer. I got it with your suggestion. The only thing is that in addition of lote1, lote2, and lote3, I am also getting an extra data frame `lote` without number. ...
written 7 months ago by Fersal20
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Using variables into data frame names in R
... I have several text files (animal_grp1.txt, animal_grp2.txt...animal_grp50.txt) I want to import and modify in R by using a for loop. I usually do this: lote1 <- read.delim("animal_grp1.txt", header = T, sep = "\t") lote1 <- lote1[c(2,5,7)] names(lote1) <- c("ID", "race", "ag ...
R loop written 7 months ago by Fersal20 • updated 7 months ago by russhh4.4k
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Comment: C: Error when indexing a bcf file
... Thank you very much to help me to solve this issue! This is the command I finally used: bcftools view -e "SUM(FORMAT/DP[0-39])>1514" -Ob myfile.bcf > my_filtered_file.bcf ...
written 9 months ago by Fersal20
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Comment: C: Error when indexing a bcf file
... The same result as with `filter` function. My VCF files have 40 samples, I understand that DP is the sum of the depth values of all those 40 samples as the header states: ##INFO= I previously know the number of SNP that have DP<1514 from the output file obtained with `--site-depth` in vcf ...
written 9 months ago by Fersal20
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Comment: C: Error when indexing a bcf file
... I don't sure whether I did it in the proper manner, but I saw in the first 1000 lines of one of my VCF files and in the column FILTER there are only dots, no PASS there. ...
written 9 months ago by Fersal20
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Comment: C: Error when indexing a bcf file
... In the case of `query` I am getting the same message `query:invalid option -- 'O'` In the case of `filter` it works but I am getting a file with less than 1 million of SNPs and I know there are around 3 millions of SNPs with DP<1514 in the original file (myfile.bcf) which has in total ~3.2 milli ...
written 9 months ago by Fersal20
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Comment: C: Error when indexing a bcf file
... I get this output: > query: invalid option -- 'O' > > About: Extracts fields from VCF/BCF file and prints them in > user-defined format Usage: bcftools query [options] > [ [...]] ... I don't know what is going on with this ...
written 9 months ago by Fersal20

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