percCellQualControl         package:RNAither         R Documentation

_Q_u_a_l_i_t_y _c_o_n_t_r_o_l _o_f _t_h_e _p_e_r_c_e_n_t_a_g_e _o_f _c_e_l_l_s

_D_e_s_c_r_i_p_t_i_o_n:

     Plots a histogram of the percentage of cells per well (ratio of
     the number of identified cells and the number of identified
     objects) and allows the user to set an upper and a lower threshold
     so as to exclude wells from the analysis.

_U_s_a_g_e:

     percCellQualControl(DataSetFile, nbLinesHeader, plotTitle)

_A_r_g_u_m_e_n_t_s:

DataSetFile: a dataset file generated with 'generateDatasetFile' 

nbLinesHeader: typically 3 

plotTitle: the plot title 

_V_a_l_u_e:

     Prints out the list of wells under and over the predefined
     thresholds in the shell.

     Saves a list of discarded siRNA values (if applicable) in a text
     file named after the experiment name specified in the header
     concatenated with either
     "percCellQualControl_discarded_higher.txt" or
     "percCellQualControl_discarded_lower.txt".

     Saves the histogram with the applied thresholds in a pdf file
     named after the experiment name specified in the header
     concatenated with the ' plotTitle'.

     Overwrites the given ' DataSetFile' with the new dataset.

_S_e_e _A_l_s_o:

     'numCellQualControl'

_E_x_a_m_p_l_e_s:

     data(exampleHeader, package="RNAither")
     data(exampleDataset, package="RNAither")
     saveDataset(header, dataset, "save_testfile1.txt")

     percCellQualControl("save_testfile1.txt", 3, "Histogram of the number of cells")
     n
     y
     n
     n

