User: blacktomato27

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Posts by blacktomato27

<prev • 55 results • page 1 of 6 • next >
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how to depict or draw inherited chromosome segments among individuals based on SNP genotyping data?
... Hi to all good afternoon I have SNP genotyping on F1 (Hybrid) and some times on parents also and format is like A/T, G/C,A/C,A/G with SNP physical positions and chromosome number. Now i would like draw which portion of genome inherited or conserved in all these individuals from their parents so th ...
genome R snp written 4 weeks ago by blacktomato2760 • updated 7 days ago by Biostar ♦♦ 20
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how to impute genetic position of SNPs based on neighboring SNPs genetic positions?
... Hi to all I have toy data like this Marker Centi morgans ---------- SNP1 2 ---------- SNP2 3.8 ---------- SNP3 ---------- SNP4 4.7 ---------- SNP5 6.2 ---------- Now i would like to know or impute genetic position of SNP3 based o ...
R impute snp written 3 months ago by blacktomato2760
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Comment: C: how to compare 1st row and 1st column value with rest of the row values in R?
... Dear Friederike Good Morning Hope you are doing good, Thanks lot for your help in solving my query. i have small query again to guess parents marker genotype based on marker data of their progeny because some times i am getting NA'a and Het (A/G,A/T,A/C,G/A,G/T,G/C, T/A,T/C,T/G,C/A,C/T,C/G) in seco ...
written 3 months ago by blacktomato2760
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how to impute or predict parent genotype based on progeny genotypic data?
... Hi to all good afternoon I have genotype data of backcross progeny along with their parents for SNP markers. Now my problem is i got missing or heterozygous status for some SNP markers in P2 (second parent) now i want to impute or predict P2 data based on progeny genotypic data. i would like to ar ...
R snp written 4 months ago by blacktomato2760 • updated 3 months ago by Biostar ♦♦ 20
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Comment: C: R providing row numbers instead row names with read.csv?
... Hi friederike Good Morning Sorry for my not fine post here, i do not know how to post perfectly and thanks for your suggestion. Actually i want to one extra column (POP) in file1 based on INDIVIDUAL COLUMN from file2. please check this link for my example files and code code - https://www.dropbox.c ...
written 5 months ago by blacktomato2760
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Comment: C: R providing row numbers instead row names with read.csv?
... dear sam Thanks for your reply, its is reading row names when i use row.names=1 i am getting like this MALE FEMALE RED A/A A/A RED1 T/T T/T RED2 C/C C/C RED3 G/G G/G RED4 A/A A/A RED5 T/T T/T but when i tried head(df) it is not showing my first column name and i am unab ...
written 5 months ago by blacktomato2760
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Comment: C: R providing row numbers instead row names with read.csv?
... hi manaswwm this is how my data in file INDIVIDUAL MALE FEMALE RED A/A A/A RED1 T/T T/T RED2 C/C C/C RED3 G/G G/G RED4 A/A A/A RED5 T/T T/T and if i tried head(df) i am getting like this INDIVIDUAL MALE FEMALE 1 RED A/A A/A 2 RED1 T/T T/T 3 RED2 C/C C/C 4 RED3 ...
written 5 months ago by blacktomato2760
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R providing row numbers instead row names with read.csv?
... Hi to all i am reading my csv files into R with read.csv function and i did it and tried to see row names of the imported file and i am getting row names like numbers like this "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13", but my row names are like this `RED, RED1, RED2, ...
R written 5 months ago by blacktomato2760 • updated 5 months ago by zx87549.7k
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how to map every SNP flanking sequences to a reference genome?
... Hi to all Good Afternoon I selected some 1000 snps based on MAF, PIC and their coverage in genome based on physical distance. Now i would like to know where and how many places are my SNP flanking sequences match or hit in reference genome? here my goal is to further select snp with only 1 hit, it m ...
alignment sequence snp blast written 7 months ago by blacktomato2760 • updated 6 months ago by Biostar ♦♦ 20
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Comment: C: how to concetanate column values of a data frame and converting single letters o
... Dear cpad0112 good afternoon Thanks for your kind and prompt reply to my request. I do not know why this below step is not working on my data but it is working on example data i provided in dropbox **mutate_at(vars(-c("LOCUS":"ALLELE","chr","MAR","MAF":"TOPsegsite[A/B]")),~str_replace_all(., "NA", R ...
written 7 months ago by blacktomato2760

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Epic Question 9 weeks ago, created a question with more than 10,000 views. For How to extract rows from data frame with row names in R?
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