pandas - How to calculate and add an FDR column to file in python -


i have following input file (input.xls):

 mouse   no_neigh_mouse  human   no_neigh_hum    intersection    totalgenetested gm20645 1   lnc3    2   1   8 gm20645 1   lnc2    1   0   8 gm20645 1   lnc1    2   1   8 gm26549 2   lnc3    2   1   8 gm26549 2   lnc2    1   1   8 gm26549 2   lnc1    2   1   8

i to:

  1. calculate hypergeom p-value each row (done successfully)
  2. then calculate fdr (which same bh) p-value corrections
  3. add adjusted p-value last column.

my expected output file have 4 columns. first value of "mouse", second value of "human", third "hypergeom-pvalue", fourth "adjusted-pvalue". able generate first 3 columns using following code:

output=open("hypergeom.xls", "w") output.write("mouse\thuman\thypergeom-pvalue\tadjusted-pvalue\n") input = pd.read_table("input.xls", sep="\t")  in range (0, len(input.index)):     hyperg= scipy.stats.hypergeom.sf(input.ix[i,4], input.ix[i,5], input.ix[i,1], input.ix[i,3],1) #calculates hypergeom p value without problem     newline = input.ix[i,0], input.ix[i,2], str(hyper)     output.write('\t'.join(newline)+'\n')     output.close()

till here, scripts works fine , following output file ("hypergeom.xls"):

 mouse   human   hypergeom-pvalue    adjusted-pvalue gm20645 lnc3    0.25 gm20645 lnc2    1 gm20645 lnc1    0.25 gm26549 lnc3    0.464285714 gm26549 lnc2    0.25 gm26549 lnc1    0.464285714

i aimed @ reopening output file input , calculate fdr based on command suggested 1 of users utilizes r: how implement r's p.adjust in python

my code then:

import rpy2.robjects r pvaluefile = pd.read_table("hypergeom.xls", sep="\t") pvalue_list = pvaluefile.ix[:,2].tolist()  #converts value column series list #now, try apply command link above p_adjusted = r['p.adjust'](r.floatvector(pvalue_list),method='bh') v in p_adjusted:     print v

i error @ step p_adjusted = r [...]. error is: typeerror: 'module' object has no attribute 'getitem'

hence, have 2 problems:

  1. i cant figure out how calculate fdr overcoming error
  2. how can add fdr column @ end of file fourth column?


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