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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 17:33 by mkatari