hapsburg.PackagesSupport.roh_expectations
=========================================

.. py:module:: hapsburg.PackagesSupport.roh_expectations


Classes
-------

.. autoapisummary::

   hapsburg.PackagesSupport.roh_expectations.Expected_Roh


Module Contents
---------------

.. py:class:: Expected_Roh

   Class that calculates expected ROH


   .. py:attribute:: chr_lgts
      :value: [2.8426, 2.688187, 2.232549, 2.14201, 2.040477, 1.917145, 1.871491, 1.680018, 1.661367,...



   .. py:method:: roh_pdf_rel(x, chr_l, m)

      Gives back the pdfs for Blocks of Length l [Morgan]
      on a Chromosome of Length [Morgan].
      m: Nr of Meiosis.
      Return PDF (per Morgan)



   .. py:method:: roh_pdf_allchr_rel(x, chr_lgts, m)

      Calculate the PDF of ROH blocks of length x [Morgan]
      for m Recombination events summed over Chromosome Lengths
      x: Can be Array
      chr_lgts: Array of all chromosome lengths [in Morgan]
      Return PDF (per Morgan)



   .. py:method:: coal_prob_rel(m, comm_anc=1)

      Calculate Coalescence Probability.
      m: Nr of Meiosis
      comm_anc: How many common ancestors



   .. py:method:: exp_roh_ind_rel(x, m, comm_anc=1, chr_lgts=[])

      Calculates the Expected density of ROH Blocks per Morgan at x M
      for full Individual
      x: Array of Block Lenths
      m: Nr of Meisois
      comm_anc: Nr of Ancestry Loops



   .. py:method:: exp_roh_len_in_bin_rel(l=[0, 3], m=6, comm_anc=4, bins=1000)

      Calculate Epected Block Length for Individual m Meisosis apart and
      with comm_anc haplotypes in common within interval l [in Morgan].
      bins: Number of linearly spaced bins to do.
      Return Sum [in Morgan]



   .. py:method:: roh_pdf_N(x, chr_l, N)

      Gives back the pdfs for Blocks of Length l [Morgan]
      on a Chromosome of Length [Morgan].
      m: Nr of Meiosis.
      Return PDF (per Morgan)



   .. py:method:: roh_pdf_allchr_N(x, chr_lgts=[], N=1000)

      Calculate the PDF of ROH blocks of length x [Morgan]
      for pop size N summed over Chromosome Lengths
      x: Can be Array
      N: effective population size (stands in for 2N)
      chr_lgts: Array of all chromosome lengths [in Morgan]
      Return PDF (per Morgan)



   .. py:method:: exp_roh_len_in_bin_N(l=[0, 3], bins=1000, N=500, chr_lgts=[])

      Calculate Epected Block Length for Individual in
      panmictic population of size N and within interval l [in Morgan].
      bins: Number of linearly spaced bins to do.
      N: Population size of haploids
      Return Sum [in Morgan]



   .. py:method:: var_roh_len_in_bin_N(l=[0, 3], bins=1000, N=500, chr_lgts=[])

      Calculate Variance of Sum ROH for Individual in
      panmictic population of size N and within interval l [in Morgan].
      bins: Number of linearly spaced bins to do.
      N: Population size of haploids
      Return Variance of Sum [in Morgan]



   .. py:method:: roh_pdf_t_N(x, chr_l, t, N)

      Calculate the PDF of ROH blocks of length x [Morgan] dx
      and time t dt
      x: Can be Array
      N: Population size (sometimes stands in for 2N)
      chr_lgts: Array of all chromosome lengths [in Morgan]
      Return PDF (per Morgan)



   .. py:method:: roh_pdf_allchr_t_N(x, chr_lgts=[], t=100, N=1000)

      Calculate the PDF of ROH blocks of length x [Morgan]
      for pop size N summed over Chromosome Lengths
      x: Can be Array
      t: Density with respect to time of origin of ROH
      chr_lgts: Array of all chromosome lengths [in Morgan]
      Return PDF (per Morgan)