filter gene expression matrix

I have a expression table in this format

Geneid  1-FPKM  2-FPKM  3-FPKM  1-T-GB3-FPKM    1-T-GM58-FPKM   1-T-MB43-FPKM   34-O-GB3-FPKM   34-O-GM58-FPKM  34-O-MB43-FPKM  34-T-GB3-FPKM   34-T-GM58-FPKM  34-T-MB43-FPKM
A00218.v2.0 0   0   0   0   0   0.090523725 0   0   0   0   0   0
A00223.v2.0 0   1.09881251  0   0   0.578112669 0.337275538 0.625452544 1.409278785 0.204600602 0   0.051926075 0
A00226.v2.0 0   0   0   0   0   0   0   0   0   0   0   0

output:

A00223.v2.0 0   1.09881251  0   0   0.578112669 0.337275538 0.625452544 1.409278785 0.204600602 0   0.051926075 0

how I can filter genes with FPKM over 1 and also available in at least one sample?

Thanks

gene-expression filter

• 1,999 views • link

updated 4.8 years ago by Ram

• written 7.5 years ago by Sam

Please show what have you tried?

• 1 views • link

written 7.5 years ago by Santosh Anand

1 answer

$ awk -v FS="\t" 'NR>1 { for(i=2;i<=NF;i++) { if($i>=1) { print; break; }}}' input_file

From the second line onwards awk iterate over all sample fields in the line. If one value is greater or equal to 1 the line is printed and we step to the next line.

For readability reasons you can put the awk code in an extra file, e.g. filter.awk

NR>1 { 
    for(i=2; i<=NF; i++) { 
        if($i>=1) { 
            print; 
            break;
        }
    }
}

Run awk like this:

$ awk -v FS="\t" -f filter.awk input_file

fin swimmer

• 1 views • link

written 7.5 years ago by finswimmer