findRegions               package:ACME               R Documentation

_F_i_n_d _a_l_l _r_e_g_i_o_n_s _i_n _d_a_t_a _a_b_o_v_e _p-_v_a_l_u_e _t_h_r_e_s_h_o_l_d

_D_e_s_c_r_i_p_t_i_o_n:

     After the ACME calculation, each probe is associated with a
     p-value of enrichment.  However, one often wants the contiguous
     regions associated with runs of p-values above a given p-value
     threshold.

_U_s_a_g_e:

     findRegions(calcobj, thresh = 1e-04)

_A_r_g_u_m_e_n_t_s:

 calcobj: An 'aGFFCalc' object

  thresh: The p-value threshold

_D_e_t_a_i_l_s:

     Runs of p-values above the p-value threshold will be reported as
     one "region".  These can be used for downstream analyses, export
     to browsers, submitted for transcription factor binding enrichment
     analyses, etc.

_V_a_l_u_e:

     A data frame with these columns: 

  Length: The length of the region in probes

      TF: Either TRUE or FALSE; TRUE regions represent regions of
          enrichment while FALSE regions are the regions between the
          TRUE regions

StartInd: The starting Index of the region

  EndInd: The ending Index of the region

  Sample: The sample containing the region

Chromosome: The Chromosome of the region

   Start: The starting basepairof the region

     End: The ending basepair of the region

_A_u_t_h_o_r(_s):

     Sean Davis <sdavis2@mail.nih.gov>

_S_e_e _A_l_s_o:

     'do.aGFF.calc', 'findClosestGene'

_E_x_a_m_p_l_e_s:

     data(example.agff)
     example.agffcalc <- do.aGFF.calc(example.agff,window=1000,thresh=0.9)
     foundregions <- findRegions(example.agffcalc,thresh=0.001)
     foundregions[1:6,]

