User: Famf

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Famf20
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Posts by Famf

<prev • 17 results • page 1 of 2 • next >
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When a chi-square value is indicating a genotyping error rather than segregation distortion signal?
... I am using chi-square test to search signals of segregation distortion in a large SNP data set genotyped in large population. Into my results there are many SNPs that look more like genotyping errors rather than segregation distortion signals. Eg. parents AA x AB => progeny 97 AA : 3 AB. As resul ...
chi square snp written 10 weeks ago by Famf20
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ambiguous characters are not reported in Bowtie2 alignments
... I am trying to align a set of read sequences (SNP chip array) to a reference genome. I want to get the physical positions of each SNP in each read. My reads are in FASTA format, e.g. >id00001Zh:Chr02:57,645,640 TGCAGACYCAGACAAGGTTTAACACAGATTGGAACCGTTA >id00002Zh:Chr07:53,650,79 ...
alignment written 3 months ago by Famf20
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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 10 months ago by Famf20
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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 10 months ago by Famf20
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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 10 months ago by Famf20 • updated 10 months ago by ATpoint23k
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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 12 months ago by Famf20
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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 12 months ago by Famf20 • updated 12 months ago by russhh4.7k
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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 13 months ago by Famf20
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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 13 months ago by Famf20
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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 13 months ago by Famf20

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