66 lines
1.7 KiB
R
66 lines
1.7 KiB
R
#=========================
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# Count Sensitivity
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# Mutations and positions
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#=========================
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pos_colname_c ="position"
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sensP_df = merged_df3[,c("mutationinformation",
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#"position",
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pos_colname_c,
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"sensitivity")]
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head(sensP_df)
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table(sensP_df$sensitivity)
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#--------------------------
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# Total unique positions
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#--------------------------
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tot_mut_pos = length(unique(sensP_df[[pos_colname_c]]))
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cat("\nNo of Tot muts sites:", tot_mut_pos)
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cat("\nThese are:", unique(sensP_df[[pos_colname_c]]))
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# resistant mut pos
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sens_site_allR = sensP_df[[pos_colname_c]][sensP_df$sensitivity=="R"]
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sens_site_UR = unique(sens_site_allR)
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length(sens_site_UR)
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# Sensitive mut pos
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sens_site_allS = sensP_df[[pos_colname_c]][sensP_df$sensitivity=="S"]
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sens_site_US = unique(sens_site_allS)
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length(sens_site_UR)
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#---------------
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# Common Sites
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#----------------
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common_pos = intersect(sens_site_UR,sens_site_US)
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site_Cc = length(common_pos)
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cat("\nNo of Common sites:", site_Cc
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, "\nThese are:", sort(unique(common_pos)))
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#---------------
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# Resistant muts
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#----------------
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site_R = sens_site_UR[!sens_site_UR%in%common_pos]
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site_Rc = length(site_R)
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if ( length(sens_site_allR) == table(sensP_df$sensitivity)[['R']] ){
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cat("\nNo of R muts:", length(sens_site_allR)
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, "\nNo. of R sites:",site_Rc
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, "\nThese are:", site_R
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)
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}
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#---------------
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# Sensitive muts
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#----------------
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site_S = sens_site_US[!sens_site_US%in%common_pos]
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site_Sc = length(site_S)
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if ( length(sens_site_allS) == table(sensP_df$sensitivity)[['S']] ){
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cat("\nNo of S muts:", length(sens_site_allS)
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, "\nNo. of S sites:", site_Sc
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, "\nThese are:", site_S)
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}
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#########################
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