User Tools

Site Tools


Back to Manny's Bioinformatics Workshop HOME

Clean SNP file

Read the file making sure explicitly tell it to delimit using tab and header is true Remember to save the file as a tab delimited text file.

read.table("Draft sent to Manny.txt", sep="\t", header=T, row.names=1)->draft

To count na use The number of True can be counted.

apply(, 2, sum) ->

Identify columns that have ⇐ 7% of missing data

draft[ ,which( <= 0.07*nrow(draft)) ] -> draft.goodsnps

Do same for genotype

apply(, 1, sum) ->

To remove the regions column and only save the snps.


Check frequency of the different alleles

mkatari-bioinformatics-august-2013-cleansnp.txt · Last modified: 2013/08/19 14:33 by mkatari