4 hours ago by
Hi friends!!!
I have a relative abundance table where samples are in column and rows contain the features (pathways). Something like this (reproducible example):
# Pathway ERR300139_Abundance-RELAB ERR267324_Abundance-RELAB ERR341905_Abundance-RELAB ERR092237_Abundance-RELAB
1CMET2-PWY: N10-formyl-tetrahydrofolate biosynthesis 0.00826631 0.00946472 0.00962571 0.00411153
3-HYDROXYPHENYLACETATE-DEGRADATION-PWY: 4-hydroxyphenylacetate degradation 0 0 0 0.000695608
7ALPHADEHYDROX-PWY: cholate degradation (bacteria, anaerobic) 0 0 0 0
AEROBACTINSYN-PWY: aerobactin biosynthesis 0 0 0 0
ALLANTOINDEG-PWY: superpathway of allantoin degradation in yeast 3.32E-05 0 3.35E-05 0
ANAEROFRUCAT-PWY: homolactic fermentation 0.00682776 0.00681683 0.00675732 0.00495716
ANAGLYCOLYSIS-PWY: glycolysis III (from glucose) 0.00866693 0.0100437 0.00829714 0.00524566
ARG+POLYAMINE-SYN: superpathway of arginine and polyamine biosynthesis 0.00106395 0.000544088 0.000774645 0.00370237
ARGDEG-PWY: superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation 0 0 0 0.00164625
ARGININE-SYN4-PWY: L-ornithine de novo biosynthesis 0.00166327 0.00383993 0.000105528 0.00230283
ARGORNPROST-PWY: arginine, ornithine and proline interconversion 0.000132331 0.000244069 7.96E-05 0.000479006
ARGSYN-PWY: L-arginine biosynthesis I (via L-ornithine) 0.0124159 0.00955758 0.0118644 0.00533077
Now, I want to keep features (i.e. pathways) which are present with abundance >0.0001 and present in at least 10% of samples. Can you please tell me how can I do that?
Thanks,
dpc
